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Logo of nihpaAbout Author manuscriptsSubmit a manuscriptHHS Public Access; Author Manuscript; Accepted for publication in peer reviewed journal;
Nat Struct Mol Biol. Author manuscript; available in PMC 2009 November 1.
Published in final edited form as:
Nat Struct Mol Biol. 2008 November; 15(11): 1213–1220.
Published online 2008 October 5. doi: 10.1038/nsmb.1496

Figure 2

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IRF5 dimer. (a) A ribbon diagram of the crystallographic IRF5 dimer is shown with one subunit in blue and one in green. Putative phosphorylation sites are shown as yellow balls. The C-terminal region lays across the surface of the second subunit making extensive contacts particularly involving helix 4, helix 5 and the interhelical region interacting with helix 2′ and loops L1′, L3′ and L5′. (Primes designate the second subunit.) (b) An expanded view of the major interacting region between subunits, rotated from a. Color code is the same as in a with key side chains shown, including those of putative phosphorylation sites with yellow carbon atoms. A hydrophobic patch on Helix 2′, formed from residues Y303′, L307′, V310′ and L403′ interacts with residues I431, L433 and I435 from the extended peptide between helices 4 and 5. Ionic interactions are contributed by residues in helix 5, including D442 with R353′, K441 with E354′ and K449 with D309′ and D312′; likely hydrogen bonds are shown as dashed lines. (c) Interface helix capping of helices 3 and 4. K401′ forms a likely hydrogen bond with the F372 carbonyl at the C-terminus of helix 3. Q373 forms a likely intrasubunit hydrogen bond with the F420 carbonyl at the C-terminus of helix 4, whereas R247′ forms a likely hydrogen bond with the main-chain carbonyl oxygen of S421. These interactions may stabilize the shorter length of helix 4 in dimeric IRF5 compared with monomeric IRF3. (d) Fo-Fc simulated annealing omit map showing the dimeric interactions of S436 with R328’ and D442 with R353′, whose atoms were removed from the atomic model for the simulated annealing process. Electron density is shown at the 3σ level. The interaction between R328′ and S436 is likely to be strengthened by phosphorylation of S436.

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