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author:("carlos, Karl")
1.  Crystal Structure of the Herpesvirus Nuclear Egress Complex Provides Insights into Inner Nuclear Membrane Remodeling 
Cell Reports  2015;13(12):2645-2652.
Summary
Although nucleo-cytoplasmic transport is typically mediated through nuclear pore complexes, herpesvirus capsids exit the nucleus via a unique vesicular pathway. Together, the conserved herpesvirus proteins pUL31 and pUL34 form the heterodimeric nuclear egress complex (NEC), which, in turn, mediates the formation of tight-fitting membrane vesicles around capsids at the inner nuclear membrane. Here, we present the crystal structure of the pseudorabies virus NEC. The structure revealed that a zinc finger motif in pUL31 and an extensive interaction network between the two proteins stabilize the complex. Comprehensive mutational analyses, characterized both in situ and in vitro, indicated that the interaction network is not redundant but rather complementary. Fitting of the NEC crystal structure into the recently determined cryoEM-derived hexagonal lattice, formed in situ by pUL31 and pUL34, provided details on the molecular basis of NEC coat formation and inner nuclear membrane remodeling.
Graphical Abstract
Highlights
•Both components of the nuclear egress complex, pUL31 and pUL34, have a unique fold•pUL31 has a conserved C3H zinc finger motif•The nuclear egress complex is highly stable with an extensive interaction surface•Molecular basis of interactions to assemble a curved hexagonal lattice coat is revealed
Herpesvirus capsids exit the nucleus by a vesicular transport through the nuclear double membrane. Zeev-Ben-Mordehai et al. present the crystal structure of the coat proteins mediating envelopment of capsids. The structure is used to model the assembly of hexagonal lattice driving vesicle formation at the inner nuclear membrane.
doi:10.1016/j.celrep.2015.11.008
PMCID: PMC4700048  PMID: 26711332
2.  Structure and functional properties of Norrin mimic Wnt for signalling with Frizzled4, Lrp5/6, and proteoglycan 
eLife  null;4:e06554.
Wnt signalling regulates multiple processes including angiogenesis, inflammation, and tumorigenesis. Norrin (Norrie Disease Protein) is a cystine-knot like growth factor. Although unrelated to Wnt, Norrin activates the Wnt/β-catenin pathway. Signal complex formation involves Frizzled4 (Fz4), low-density lipoprotein receptor related protein 5/6 (Lrp5/6), Tetraspanin-12 and glycosaminoglycans (GAGs). Here, we report crystallographic and small-angle X-ray scattering analyses of Norrin in complex with Fz4 cysteine-rich domain (Fz4CRD), of this complex bound with GAG analogues, and of unliganded Norrin and Fz4CRD. Our structural, biophysical and cellular data, map Fz4 and putative Lrp5/6 binding sites to distinct patches on Norrin, and reveal a GAG binding site spanning Norrin and Fz4CRD. These results explain numerous disease-associated mutations. Comparison with the Xenopus Wnt8–mouse Fz8CRD complex reveals Norrin mimics Wnt for Frizzled recognition. The production and characterization of wild-type and mutant Norrins reported here open new avenues for the development of therapeutics to combat abnormal Norrin/Wnt signalling.
DOI: http://dx.doi.org/10.7554/eLife.06554.001
eLife digest
The cells within an animal need to be able to communicate with each other to coordinate many complex processes in the body, such as the formation of tissues and organs. One way in which the cells can communicate is through a pathway called Wnt signalling. Generally, one cell releases a protein called Wnt, which binds to a receptor protein called Frizzled that sits on the surface of the same or another cell. This activates a series of events in the cells that can change the activity of particular genes. Wnt signalling has many roles in animals, and defects in it can contribute to cancer and other devastating diseases.
Another protein called Norrin can also activate Wnt signalling by binding to Frizzled and another receptor protein called Lrp5/6. This group or ‘complex’ also includes molecules called glycosaminoglycans. In humans, mutations in the gene that encodes Norrin can cause a disease in which blood vessels in the eye fail to form correctly, which can result in blindness. However, it is not clear how Norrin activates Wnt signalling.
Chang et al. developed a method to produce large quantities of Norrin protein to allow them to study the structure of the protein. Then, a technique called X-ray crystallography was used to reveal the three-dimensional structure of Norrin when it is bound to Frizzled. The model reveals that a pair of Norrin proteins form a complex with two Frizzled proteins and highlights particular areas of the Norrin protein that interact with Frizzled. Molecules of glycosaminoglycan bind to a site in the complex that spans both Norrin and Frizzled. The model also predicts that other areas of the Norrin protein may be involved in binding Lrp5/6.
Chang et al. compared the model to the structure of a Wnt protein bound to Frizzled, which revealed that Norrin and Wnt show some fundamental similarities in the way they bind to Frizzled. These findings move us closer to defining the essential features of the protein complexes that modify Wnt signalling, and may aid the development of new therapies for diseases that affect the development of the eye.
DOI: http://dx.doi.org/10.7554/eLife.06554.002
doi:10.7554/eLife.06554
PMCID: PMC4497409  PMID: 26158506
Wnt signalling; cystine-knot growth factor; retinal disease; angiogenesis; crystal structure; blood brain barrier; human; mouse
3.  Structural Basis of Latrophilin-FLRT Interaction 
Structure(London, England:1993)  2015;23(4):774-781.
Summary
Latrophilins, receptors for spider venom α-latrotoxin, are adhesion type G-protein-coupled receptors with emerging functions in synapse development. The N-terminal region binds the endogenous cell adhesion molecule FLRT, a major regulator of cortical and synapse development. We present crystallographic data for the mouse Latrophilin3 lectin and olfactomedin-like (Olf) domains, thereby revealing the Olf β-propeller fold and conserved calcium-binding site. We locate the FLRT-Latrophilin binding surfaces by a combination of sequence conservation analysis, point mutagenesis, and surface plasmon resonance experiments. In stripe assays, we show that wild-type Latrophilin3 and its high-affinity interactor FLRT2, but not the binding-impaired mutants we generated, promote HeLa cell adhesion. In contrast, cortical neurons expressing endogenous FLRTs are repelled by wild-type Latrophilin3 and not by the binding-impaired mutant. Taken together, we present molecular level insights into Latrophilin structure, its FLRT-binding mechanism, and a role for Latrophilin and FLRT that goes beyond a simply adhesive interaction.
Graphical Abstract
Highlights
•The LPHN olfactomedin-like domain forms a five-bladed β propeller•A conserved calcium-binding site is located at the center of the protein•Latrophilin-FLRT binding depends on a conserved binding site•Mutations in the binding site inhibit Latrophilin-FLRT signaling
Jackson et al. describe a crystal structure of mLPHN3 lectin and olfactomedin-like (Olf) domains, revealing the Olf β-propeller fold and calcium-binding site. Assays using HeLa cells and cortical neurons reveal a bi-functional role for Olf and its ligand FLRT, leading to HeLa cell adhesion and neuron repulsion.
doi:10.1016/j.str.2015.01.013
PMCID: PMC4396693  PMID: 25728924
4.  Structural Basis for the Activity of a Cytoplasmic RNA Terminal U-transferase 
Cytoplasmic terminal uridylyltransferases (TUTases) comprise a conserved family of enzymes that negatively regulate the stability or biological activity of a variety of eukaryotic RNAs, including mRNAs and tumor suppressor let-7 miRNAs. Here we describe crystal structures of the Schizosaccharomyces pombe TUTase Cid1 in two Apo conformers and bound to UTP. We demonstrate that a single histidine residue, conserved in mammalian Cid1 orthologs, is responsible for discrimination between UTP and ATP. We also describe a novel high-affinity RNA substrate binding mechanism of Cid1, which is essential for its enzymatic activity and is mediated by three basic patches across the surface of the enzyme. Overall, our structures provide a basis for understanding the activity of Cid1 and a mechanism of UTP selectivity conserved in its human orthologs, with potential implications for anti-cancer drug design.
doi:10.1038/nsmb.2329
PMCID: PMC4342108  PMID: 22751018
5.  Four crystal structures of human LLT1, a ligand of human NKR-P1, in varied glycosylation and oligomerization states 
Four crystal structures of human LLT1, a ligand of human NKR-P1, are reported.
Human LLT1 is a C-type lectin-like ligand of NKR-P1 (CD161, gene KLRB1), a C-type lectin-like receptor of natural killer cells. Using X-ray diffraction, the first experimental structures of human LLT1 were determined. Four structures of LLT1 under various conditions were determined: monomeric, dimeric deglycosylated after the first N-acetylglucosamine unit in two forms and hexameric with homogeneous GlcNAc2Man5 glycosylation. The dimeric form follows the classical dimerization mode of human CD69. The monomeric form keeps the same fold with the exception of the position of an outer part of the long loop region. The hexamer of glycosylated LLT1 consists of three classical dimers. The hexameric packing may indicate a possible mode of interaction of C-type lectin-like proteins in the glycosylated form.
doi:10.1107/S1399004714027928
PMCID: PMC4356368  PMID: 25760607
LLT1; C-type lectin-like ligand
6.  Improved crystallization and diffraction of caffeine-induced death suppressor protein 1 (Cid1) 
The use of truncation and RNA-binding mutations of caffeine induced death suppressor protein 1 (Cid1) as a means to enhance crystallogenesis leading to an improvement of X-ray diffraction resolution by 1.5 Å is reported.
The post-transcriptional addition of uridines to the 3′-end of RNAs is an important regulatory process that is critical for coding and noncoding RNA stability. In fission yeast and metazoans this untemplated 3′-uridylylation is catalysed by a single family of terminal uridylyltransferases (TUTs) whose members are adapted to specific RNA targets. In Schizosaccharomyces pombe the TUT Cid1 is responsible for the uridylylation of polyadenylated mRNAs, targeting them for destruction. In metazoans, the Cid1 orthologues ZCCHC6 and ZCCHC11 uridylate histone mRNAs, targeting them for degradation, but also uridylate microRNAs, altering their maturation. Cid1 has been studied as a model TUT that has provided insights into the larger and more complex metazoan enzyme system. In this paper, two strategies are described that led to improvements both in the crystallogenesis of Cid1 and in the resolution of diffraction by ∼1.5 Å. These advances have allowed high-resolution crystallo­graphic studies of this TUT system to be initiated.
doi:10.1107/S2053230X15001351
PMCID: PMC4356314  PMID: 25760713
terminal uridylyltransferases; Cid1
7.  Structural plasticity of Cid1 provides a basis for its distributive RNA terminal uridylyl transferase activity 
Nucleic Acids Research  2015;43(5):2968-2979.
Terminal uridylyl transferases (TUTs) are responsible for the post-transcriptional addition of uridyl residues to RNA 3′ ends, leading in some cases to altered stability. The Schizosaccharomyces pombe TUT Cid1 is a model enzyme that has been characterized structurally at moderate resolution and provides insights into the larger and more complex mammalian TUTs, ZCCHC6 and ZCCHC11. Here, we report a higher resolution (1.74 Å) crystal structure of Cid1 that provides detailed evidence for uracil selection via the dynamic flipping of a single histidine residue. We also describe a novel closed conformation of the enzyme that may represent an intermediate stage in a proposed product ejection mechanism. The structural insights gained, combined with normal mode analysis and biochemical studies, demonstrate that the plasticity of Cid1, particularly about a hinge region (N164–N165), is essential for catalytic activity, and provide an explanation for its distributive uridylyl transferase activity. We propose a model clarifying observed differences between the in vitro apparently processive activity and in vivo distributive monouridylylation activity of Cid1. We suggest that modulating the flexibility of such enzymes—for example by the binding of protein co-factors—may allow them alternatively to add single or multiple uridyl residues to the 3′ termini of RNA molecules.
doi:10.1093/nar/gkv122
PMCID: PMC4357723  PMID: 25712096
8.  Expression, purification and crystallization of the ectodomain of the envelope glycoprotein E2 from Bovine viral diarrhoea virus  
The cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of the ectodomain of BVDV E2 are described.
Bovine viral diarrhoea virus (BVDV) is an economically important animal pathogen which is closely related to Hepatitis C virus. Of the structural proteins, the envelope glycoprotein E2 of BVDV is the major antigen which induces neutralizing antibodies; thus, BVDV E2 is considered as an ideal target for use in subunit vaccines. Here, the expression, purification of wild-type and mutant forms of the ectodomain of BVDV E2 and subsequent crystallization and data collection of two crystal forms grown at low and neutral pH are reported. Native and multiple-wavelength anomalous dispersion (MAD) data sets have been collected and structure determination is in progress.
doi:10.1107/S1744309112049184
PMCID: PMC3539699  PMID: 23295482
Pestivirus; BVDV; envelope glycoprotein E2
9.  FLRT Structure: Balancing Repulsion and Cell Adhesion in Cortical and Vascular Development 
Neuron  2014;84(2):370-385.
Summary
FLRTs are broadly expressed proteins with the unique property of acting as homophilic cell adhesion molecules and as heterophilic repulsive ligands of Unc5/Netrin receptors. How these functions direct cell behavior and the molecular mechanisms involved remain largely unclear. Here we use X-ray crystallography to reveal the distinct structural bases for FLRT-mediated cell adhesion and repulsion in neurons. We apply this knowledge to elucidate FLRT functions during cortical development. We show that FLRTs regulate both the radial migration of pyramidal neurons, as well as their tangential spread. Mechanistically, radial migration is controlled by repulsive FLRT2-Unc5D interactions, while spatial organization in the tangential axis involves adhesive FLRT-FLRT interactions. Further, we show that the fundamental mechanisms of FLRT adhesion and repulsion are conserved between neurons and vascular endothelial cells. Our results reveal FLRTs as powerful guidance factors with structurally encoded repulsive and adhesive surfaces.
Highlights
•Distinct FLRT surfaces mediate homophilic adhesion and Unc5-dependent repulsion•Neurons expressing Unc5 and FLRT integrate adhesive and repulsive FLRT signals•FLRTs direct radial migration and tangential spread of cortical neurons•FLRT3 controls retinal vascularization
Cortical development depends on a balance of adhesive and repulsive interactions between cells. Seiradake et al. show how FLRT proteins fine-tune adhesion and repulsion between cells migrating through the neocortex. Vascular cells are also guided by FLRT using structurally conserved mechanisms.
doi:10.1016/j.neuron.2014.10.008
PMCID: PMC4210639  PMID: 25374360
10.  Unexpected structure for the N-terminal domain of hepatitis C virus envelope glycoprotein E1 
Nature Communications  2014;5:4874.
Hepatitis C virus (HCV) infection remains a major health problem worldwide. HCV entry into host cells and membrane fusion are achieved by two envelope glycoproteins, E1 and E2. We report here the 3.5-Å resolution crystal structure of the N-terminal domain of the HCV E1 ectodomain, which reveals a complex network of covalently linked intertwined homodimers that do not harbour the expected truncated class II fusion protein fold.
Hepatitis C virus (HCV) gains entry into host cells via envelope glycoproteins E1 and E2. Here, El Omari et al. present the crystal structure of the N terminus of the E1 ectodomain of HCV and show that it adopts a different fold than predicted.
doi:10.1038/ncomms5874
PMCID: PMC4175578  PMID: 25224686
11.  Pushing the limits of sulfur SAD phasing: de novo structure solution of the N-terminal domain of the ectodomain of HCV E1 
The sulfur SAD phasing method was successfully used to determine the structure of the N-terminal domain of HCV E1 from low-resolution diffracting crystals by combining data from 32 crystals.
Single-wavelength anomalous dispersion of S atoms (S-SAD) is an elegant phasing method to determine crystal structures that does not require heavy-atom incorporation or selenomethionine derivatization. Nevertheless, this technique has been limited by the paucity of the signal at the usual X-ray wavelengths, requiring very accurate measurement of the anomalous differences. Here, the data collection and structure solution of the N-terminal domain of the ectodomain of HCV E1 from crystals that diffracted very weakly is reported. By combining the data from 32 crystals, it was possible to solve the sulfur substructure and calculate initial maps at 7 Å resolution, and after density modication and phase extension using a higher resolution native data set to 3.5 Å resolution model building was achievable.
doi:10.1107/S139900471401339X
PMCID: PMC4118829  PMID: 25084338
sulfur SAD; HCV; envelope glycoprotein E1
12.  Drastic changes in conformational dynamics of the antiterminator M2-1 regulate transcription efficiency in Pneumovirinae 
eLife  2014;3:e02674.
The M2-1 protein of human metapneumovirus (HMPV) is a zinc-binding transcription antiterminator which is highly conserved among pneumoviruses. We report the structure of tetrameric HMPV M2-1. Each protomer features a N-terminal zinc finger domain and an α-helical tetramerization motif forming a rigid unit, followed by a flexible linker and an α-helical core domain. The tetramer is asymmetric, three of the protomers exhibiting a closed conformation, and one an open conformation. Molecular dynamics simulations and SAXS demonstrate a dynamic equilibrium between open and closed conformations in solution. Structures of adenosine monophosphate- and DNA- bound M2-1 establish the role of the zinc finger domain in base-specific recognition of RNA. Binding to ‘gene end’ RNA sequences stabilized the closed conformation of M2-1 leading to a drastic shift in the conformational landscape of M2-1. We propose a model for recognition of gene end signals and discuss the implications of these findings for transcriptional regulation in pneumoviruses.
DOI: http://dx.doi.org/10.7554/eLife.02674.001
eLife digest
To produce a protein from a gene, the gene must first be transcribed to make a molecule of RNA. In general, the enzyme building the RNA molecule stops building when it reaches the end of a gene and encounters a termination signal. When a virus replicates, however, it needs to transcribe all the genes in its genome, so it relies on antiterminator proteins to make the enzyme building the RNA ignore the termination signal. Therefore, medicines that stop antiterminators working could stop viral infections spreading.
Human metapneumovirus (HMPV) can cause severe respiratory infections in children, the elderly and people with weakened immune systems. A protein called M2-1 that is found inside HMPV must be present for the virus to infect humans, and it was recently shown that this protein plays a role in antitermination in a virus closely related to HMPV.
Using a range of techniques, including X-ray crystallography and molecular dynamics simulations, Leyrat et al. worked out the structure of M2-1 in HMPV, and showed that it can flip between ‘open’ and ‘closed’ forms. The open structure presents surfaces that could be targeted by antiviral drugs. When M2-1 binds to RNA, the closed structure is stabilized as a result of the RNA binding to two separate sites on the protein.
Leyrat et al. suggest that similar antiterminator proteins in related viruses—including respiratory syncytial virus, Marburg and Ebola—could also bind in this way. Leyrat et al. also propose a model describing how M2-1 can recognize the end of a gene, which could help with the development of new antiviral treatments.
DOI: http://dx.doi.org/10.7554/eLife.02674.002
doi:10.7554/eLife.02674
PMCID: PMC4051120  PMID: 24842877
human metapneumovirus; virus transcription; RNA polymerase; structural virology; viruses; other
13.  Structural Insights into the Inhibition of Wnt Signaling by Cancer Antigen 5T4/Wnt-Activated Inhibitory Factor 1 
Structure(London, England:1993)  2014;22(4):612-620.
Summary
The tumor antigen 5T4/WAIF1 (Wnt-activated inhibitory factor 1; also known as Trophoblast glycoprotein TPBG) is a cell surface protein targeted in multiple cancer immunotherapy clinical trials. Recently, it has been shown that 5T4/WAIF1 inhibits Wnt/β-catenin signaling, a signaling system central to many developmental and pathological processes. Wnt/β-catenin signaling is controlled by multiple inhibitors and activators. Here, we report crystal structures for the extracellular domain of 5T4/WAIF1 at 1.8 Å resolution. They reveal a highly glycosylated, rigid core, comprising eight leucine-rich repeats (LRRs), which serves as a platform to present evolutionarily conserved surface residues in the N-terminal LRR1. Structural and cell-based analyses, coupled with previously reported in vivo data, suggest that Tyr325 plus the LRR1 surface centered on a second exposed aromatic residue, Phe97, are essential for inhibition of Wnt/β-catenin signaling. These results provide a structural basis for the development of 5T4/WAIF1-targeted therapies that preserve or block 5T4/WAIF1-mediated inhibition of Wnt/β-catenin signaling.
Graphical Abstract
Highlights
•High-resolution crystal structures of human cancer antigen 5T4/WAIF1•Crystal structures of 5T4/WAIF1 reveal the LRR core decorated with loops and glycans•LRRs provide a platform for evolutionarily conserved residues•Lys76, Phe97, and Tyr325 of 5T4/WAIF1 are essential for inhibition of Wnt signaling
The cell surface protein 5T4/WAIF1 is the target in multiple cancer immunotherapy clinical trials, although its mechanism of action is still obscure. Zhao et al. examine the structure and function of the extracellular domain of 5T4/WAIF1 and uncover key residues essential for the inhibition of Wnt/β-catenin signaling.
doi:10.1016/j.str.2014.01.009
PMCID: PMC3988984  PMID: 24582434
14.  Structurally encoded intraclass differences in EphA clusters drive distinct cell responses 
The functional outcomes of ephrin binding to Eph receptors (Ephs) range from cell repulsion to adhesion. Here we used cell collapse and stripe assays to show contrasting effects of human ephrinA5 binding to EphA2 and EphA4. Despite equivalent ligand-binding affinities EphA4 triggered greater cell collapse, while EphA2-expressing cells adhered better to ephrinA5-coated surfaces. Chimeric receptors showed the ectodomain is a major determinant of cell response. We report crystal structures of EphA4 ectodomain alone and in complexes with ephrinB3 and ephrinA5. These revealed closed clusters with a dimeric or circular arrangement in the crystal lattice, contrasting with extended arrays previously observed for EphA2 ectodomain. Localization microscopy-based analyses showed ligand-stimulated EphA4 induces smaller clusters than EphA2. Mutant Ephs link these characteristics to interactions observed in the crystal lattices, suggesting a mechanism by which distinctive ectodomain surfaces determine clustering, and thereby signalling, properties.
doi:10.1038/nsmb.2617
PMCID: PMC3941021  PMID: 23812375
cell adhesion; cell repulsion; receptor clustering; receptor cis interaction; Eph–ephrin crystal structures; Eph ectodomain
15.  Structure and Self-Assembly of the Calcium Binding Matrix Protein of Human Metapneumovirus 
Structure(London, England:1993)  2014;22(1):136-148.
Summary
The matrix protein (M) of paramyxoviruses plays a key role in determining virion morphology by directing viral assembly and budding. Here, we report the crystal structure of the human metapneumovirus M at 2.8 Å resolution in its native dimeric state. The structure reveals the presence of a high-affinity Ca2+ binding site. Molecular dynamics simulations (MDS) predict a secondary lower-affinity site that correlates well with data from fluorescence-based thermal shift assays. By combining small-angle X-ray scattering with MDS and ensemble analysis, we captured the structure and dynamics of M in solution. Our analysis reveals a large positively charged patch on the protein surface that is involved in membrane interaction. Structural analysis of DOPC-induced polymerization of M into helical filaments using electron microscopy leads to a model of M self-assembly. The conservation of the Ca2+ binding sites suggests a role for calcium in the replication and morphogenesis of pneumoviruses.
Highlights
•M is a calcium binding protein•Calcium stabilizes the structure of M•M forms an obligate dimer in solution•M self-assembles in the presence of lipids•The Paramyxoviruses and the Filoviruses have a common ancestor
The matrix protein (M) of paramyxoviruses plays a key role in determining virion morphology by directing viral assembly and budding. Leyrat et al. show that M forms an obligate dimer stabilized by calcium ion binding and suggest a role for Ca2+ in the replication and morphogenesis of some paramyxoviruses.
doi:10.1016/j.str.2013.10.013
PMCID: PMC3887258  PMID: 24316400
16.  Crystal Structure of Venezuelan Hemorrhagic Fever Virus Fusion Glycoprotein Reveals a Class 1 Postfusion Architecture with Extensive Glycosylation 
Journal of Virology  2013;87(23):13070-13075.
Guanarito virus (GTOV) is an emergent and deadly pathogen. We present the crystal structure of the glycosylated GTOV fusion glycoprotein to 4.1-Å resolution in the postfusion conformation. Our structure reveals a classical six-helix bundle and presents direct verification that New World arenaviruses exhibit class I viral membrane fusion machinery. The structure provides visualization of an N-linked glycocalyx coat, and consideration of glycan dynamics reveals extensive coverage of the underlying protein surface, following virus-host membrane fusion.
doi:10.1128/JVI.02298-13
PMCID: PMC3838125  PMID: 24049182
17.  Solution and Crystallographic Structures of the Central Region of the Phosphoprotein from Human Metapneumovirus 
PLoS ONE  2013;8(11):e80371.
Human metapneumovirus (HMPV) of the family Paramyxoviridae is a major cause of respiratory illness worldwide. Phosphoproteins (P) from Paramyxoviridae are essential co-factors of the viral RNA polymerase that form tetramers and possess long intrinsically disordered regions (IDRs). We located the central region of HMPV P (Pced) which is involved in tetramerization using disorder analysis and modeled its 3D structure ab initio using Rosetta fold-and-dock. We characterized the solution-structure of Pced using small angle X-ray scattering (SAXS) and carried out direct fitting to the scattering data to filter out incorrect models. Molecular dynamics simulations (MDS) and ensemble optimization were employed to select correct models and capture the dynamic character of Pced. Our analysis revealed that oligomerization involves a compact central core located between residues 169-194 (Pcore), that is surrounded by flexible regions with α-helical propensity. We crystallized this fragment and solved its structure at 3.1 Å resolution by molecular replacement, using the folded core from our SAXS-validated ab initio model. The RMSD between modeled and experimental tetramers is as low as 0.9 Å, demonstrating the accuracy of the approach. A comparison of the structure of HMPV P to existing mononegavirales Pced structures suggests that Pced evolved under weak selective pressure. Finally, we discuss the advantages of using SAXS in combination with ab initio modeling and MDS to solve the structure of small, homo-oligomeric protein complexes.
doi:10.1371/journal.pone.0080371
PMCID: PMC3817118  PMID: 24224051
18.  An extracellular steric seeding mechanism for Eph-ephrin signalling platform assembly 
Erythropoetin-producing hepatoma (Eph) receptors are cell surface protein tyrosine kinases mediating cell-cell communication. Upon activation they form signalling clusters. We report crystal structures of the full ectodomain of human EphA2 (eEphA2), alone and in complex with the receptor-binding domain of the ligand ephrinA5 (ephrinA5RBD). Unliganded eEphA2 forms linear arrays of staggered parallel receptors involving two patches of residues conserved across A-class Ephs. eEphA2-ephrinA5RBD forms a more elaborate assembly, whose interfaces include the same conserved regions on eEphA2, but re-arranged to accommodate ephrinA5RBD. Cell surface expression of mutant EphA2s demonstrated that these interfaces are critical for localization at cell-cell contacts and activation-dependent degradation. Our results suggest a ‘nucleation’ mechanism whereby a limited number of ligand-receptor interactions seed an arrangement of receptors which can propagate into extended signalling arrays.
doi:10.1038/nsmb.1782
PMCID: PMC3672960  PMID: 20228801
19.  Bacteriophage P23-77 Capsid Protein Structures Reveal the Archetype of an Ancient Branch from a Major Virus Lineage 
Structure(London, England:1993)  2013;21(5):718-726.
Summary
It has proved difficult to classify viruses unless they are closely related since their rapid evolution hinders detection of remote evolutionary relationships in their genetic sequences. However, structure varies more slowly than sequence, allowing deeper evolutionary relationships to be detected. Bacteriophage P23-77 is an example of a newly identified viral lineage, with members inhabiting extreme environments. We have solved multiple crystal structures of the major capsid proteins VP16 and VP17 of bacteriophage P23-77. They fit the 14 Å resolution cryo-electron microscopy reconstruction of the entire virus exquisitely well, allowing us to propose a model for both the capsid architecture and viral assembly, quite different from previously published models. The structures of the capsid proteins and their mode of association to form the viral capsid suggest that the P23-77-like and adeno-PRD1 lineages of viruses share an extremely ancient common ancestor.
Highlights
•High-resolution structures of the two major capsid proteins of bacteriophage P23-77•P23-77 capsid proteins exhibit a conserved single β-barrel core fold•P23-77 is an ancient relative of the double β-barrel lineage of viruses•Capsid model illustrates that P23-77 uses a novel method of organization
Rissanen et al. propose a model for the architecture and assembly of bacteriophage P23-77 quite different from those previously published. The capsid proteins and their mode of association to form the virus particle suggest that P23-77 share a common evolutionary origin with the PRD1/Adenovirus lineage.
doi:10.1016/j.str.2013.02.026
PMCID: PMC3919167  PMID: 23623731
20.  Structural Basis of Fibrillar Collagen Trimerization and Related Genetic Disorders 
Nature structural & molecular biology  2012;19(10):1031-1036.
Summary
The C-propeptides of fibrillar procollagens play crucial roles in tissue growth and repair by controlling both the intracellular assembly of procollagen molecules and the extracellular assembly of collagen fibrils. Mutations in the C-propeptides are associated with several, often lethal, genetic disorders affecting bone, cartilage, blood vessels and skin. Here we report the first crystal structure of a C-propeptide domain, from human procollagen III. It reveals an exquisite structural mechanism of chain recognition during intracellular trimerization of the procollagen molecule. It also gives insights into why some types of collagen consist of three identical polypeptide chains while others do not. Finally, the data show striking correlations between the sites of numerous disease-related mutations in different C-propeptide domains and the degree of phenotype severity. The results have broad implications for understanding genetic disorders of connective tissues and designing new therapeutic strategies.
doi:10.1038/nsmb.2389
PMCID: PMC3465578  PMID: 23001006
21.  Structure of a Pestivirus Envelope Glycoprotein E2 Clarifies Its Role in Cell Entry 
Cell Reports  2013;3(1):30-35.
Summary
Enveloped viruses have developed various adroit mechanisms to invade their host cells. This process requires one or more viral envelope glycoprotein to achieve cell attachment and membrane fusion. Members of the Flaviviridae such as flaviviruses possess only one envelope glycoprotein, E, whereas pestiviruses and hepacivirus encode two glycoproteins, E1 and E2. Although E2 is involved in cell attachment, it has been unclear which protein is responsible for membrane fusion. We report the crystal structures of the homodimeric glycoprotein E2 from the pestivirus bovine viral diarrhea virus 1 (BVDV1) at both neutral and low pH. Unexpectedly, BVDV1 E2 does not have a class II fusion protein fold, and at low pH the N-terminal domain is disordered, similarly to the intermediate postfusion state of E2 from sindbis virus, an alphavirus. Our results suggest that the pestivirus and possibly the hepacivirus fusion machinery are unlike any previously observed.
Graphical Abstract
Highlights
► Structure of the major antigenically dominant protein of BVDV ► The overall fold of BVDV E2 shows no similarity to the class II fusion proteins ► At low pH, BVDV E2 N-terminal domain is disordered ► Entry mechanism of BVDV is probably applicable to hepatitis C virus
Stuart and colleagues have determined the atomic structure of the ectodomain of bovine viral diarrhea virus E2 glycoprotein, the major, antigenically dominant protein on the virus surface. The structure was expected to resemble the fusion molecules found on the surface of viruses such as dengue virus, but it is unlike anything previously seen. E2 itself is not, in fact, the fusion protein but binds the cell receptor and directs fusion via a pH-dependent conformational switch.
doi:10.1016/j.celrep.2012.12.001
PMCID: PMC3607223  PMID: 23273918
22.  Crystallization, dehydration and experimental phasing of WbdD, a bifunctional kinase and methyltransferase from Escherichia coli O9a 
The optimization of WbdD crystals using a novel dehydration protocol and experimental phasing at 3.5 Å resolution by cross-crystal averaging followed by molecular replacement of electron density into a non-isomorphous 3.0 Å resolution native data set are reported.
WbdD is a bifunctional kinase/methyltransferase that is responsible for regulation of lipopolysaccharide O antigen polysaccharide chain length in Escherichia coli serotype O9a. Solving the crystal structure of this protein proved to be a challenge because the available crystals belonging to space group I23 only diffracted to low resolution (>95% of the crystals diffracted to resolution lower than 4 Å and most only to 8 Å) and were non-isomorphous, with changes in unit-cell dimensions of greater than 10%. Data from a serendipitously found single native crystal that diffracted to 3.0 Å resolution were non-isomorphous with a lower (3.5 Å) resolution selenomethionine data set. Here, a strategy for improving poor (3.5 Å resolution) initial phases by density modification and cross-crystal averaging with an additional 4.2 Å resolution data set to build a crude model of WbdD is desribed. Using this crude model as a mask to cut out the 3.5 Å resolution electron density yielded a successful molecular-replacement solution of the 3.0 Å resolution data set. The resulting map was used to build a complete model of WbdD. The hydration status of individual crystals appears to underpin the variable diffraction quality of WbdD crystals. After the initial structure had been solved, methods to control the hydration status of WbdD were developed and it was thus possible to routinely obtain high-resolution diffraction (to better than 2.5 Å resolution). This novel and facile crystal-dehydration protocol may be useful for similar challenging situations.
doi:10.1107/S0907444912029599
PMCID: PMC3447403  PMID: 22993091
WbdD; crystal dehydration
23.  Crystallization and preliminary crystallographic analysis of the major capsid proteins VP16 and VP17 of bacteriophage P23-77 
The major capsid proteins VP16 and VP17 of bacteriophage P23-77 have been crystallized using both recombinant and purified virus and preliminary diffraction analyses have been performed.
Members of the diverse double-β-barrel lineage of viruses are identified by the conserved structure of their major coat protein. New members of this lineage have been discovered based on structural analysis and we are interested in identifying relatives that utilize unusual versions of the double-β-barrel fold. One candidate for such studies is P23-77, an icosahedral dsDNA bacteriophage that infects the extremophile Thermus thermophilus. P23-77 has two major coat proteins, namely VP16 and VP17, of a size consistent with a single-β-barrel core fold. These previously unstudied proteins have now been successfully expressed as recombinant proteins, purified and crystallized using hanging-drop and sitting-drop vapour-diffusion methods. Crystals of coat proteins VP16 and VP17 have been obtained as well as of a putative complex. In addition, virus-derived material has been crystallized. Diffraction data have been collected to beyond 3 Å resolution for five crystal types and structure determinations are in progress.
doi:10.1107/S1744309112010330
PMCID: PMC3374517  PMID: 22691792
bacteriophages; capsid proteins
24.  In situ macromolecular crystallography using microbeams 
A sample environment for mounting crystallization trays has been developed on the microfocus beamline I24 at Diamond Light Source. The technical developments and several case studies are described.
Despite significant progress in high-throughput methods in macromolecular crystallography, the production of diffraction-quality crystals remains a major bottleneck. By recording diffraction in situ from crystals in their crystallization plates at room temperature, a number of problems associated with crystal handling and cryoprotection can be side-stepped. Using a dedicated goniometer installed on the microfocus macromolecular crystallography beamline I24 at Diamond Light Source, crystals have been studied in situ with an intense and flexible microfocus beam, allowing weakly diffracting samples to be assessed without a manual crystal-handling step but with good signal to noise, despite the background scatter from the plate. A number of case studies are reported: the structure solution of bovine enterovirus 2, crystallization screening of membrane proteins and complexes, and structure solution from crystallization hits produced via a high-throughput pipeline. These demonstrate the potential for in situ data collection and structure solution with microbeams.
doi:10.1107/S0907444912006749
PMCID: PMC4791750  PMID: 22525757
in situ diffraction; microfocus; microbeams; high throughput; room temperature; viruses; membrane proteins; synchrotron radiation
25.  Structural basis for cell surface patterning through NetrinG–NGL interactions 
The EMBO Journal  2011;30(21):4479-4488.
Structural basis for cell surface patterning through NetrinG–NGL interactions
NetrinGs and NetrinG-ligands (NGLs) control neuronal circuit development, and their dysregulation is associated with autism and schizophrenia. The first structures of NetrinG-NGL complexes and structure-based functional assays show that binding affinity governs the cell surface compartmentalization of NGLs.
Brain wiring depends on cells making highly localized and selective connections through surface protein–protein interactions, including those between NetrinGs and NetrinG ligands (NGLs). The NetrinGs are members of the structurally uncharacterized netrin family. We present a comprehensive crystallographic analysis comprising NetrinG1–NGL1 and NetrinG2–NGL2 complexes, unliganded NetrinG2 and NGL3. Cognate NetrinG–NGL interactions depend on three specificity-conferring NetrinG loops, clasped tightly by matching NGL surfaces. We engineered these NGL surfaces to implant custom-made affinities for NetrinG1 and NetrinG2. In a cellular patterning assay, we demonstrate that NetrinG-binding selectivity can direct the sorting of a mixed population of NGLs into discrete cell surface subdomains. These results provide a molecular model for selectivity-based patterning in a neuronal recognition system, dysregulation of which is associated with severe neuropsychological disorders.
doi:10.1038/emboj.2011.346
PMCID: PMC3230378  PMID: 21946559
brain patterning; crystal structure; protein engineering; schizophrenia; synaptic adhesion

Results 1-25 (35)