This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

1w5j

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 07:13, 4 April 2018

AN ANTI-PARALLEL FOUR HELIX BUNDLE

Structural highlights

1w5j is a 4 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
NonStd Res:
Related:	1ce9, 1dgc, 1env, 1fav, 1gcl, 1gcm, 1gk6, 1gzl, 1ihq, 1ij0, 1ij1, 1ij2, 1ij3, 1kql, 1ld4, 1llm, 1nkn, 1piq, 1rb1, 1rb4, 1rb5, 1rb6, 1swi, 1tmz, 1m6t, 1unt, 1unu, 1unv, 1unw, 1unx, 1uny, 1unz, 1uo0, 1uo1, 1uo2, 1uo3, 1uo4, 1uo5, 1vzl, 1ysa, 1zii, 1zij, 1zik, 1zil, 1zim, 1zta, 2dgc, 2zta, 1w5g, 1w5h, 1w5i, 1w5k, 1w5l
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

A detailed understanding of the mechanisms by which particular amino acid sequences can give rise to more than one folded structure, such as for proteins that undergo large conformational changes or misfolding, is a long-standing objective of protein chemistry. Here, we describe the crystal structures of a single coiled-coil peptide in distinct parallel and antiparallel tetrameric configurations and further describe the parallel or antiparallel crystal structures of several related peptide sequences; the antiparallel tetrameric assemblies represent the first crystal structures of GCN4-derived peptides exhibiting such a configuration. Intriguingly, substitution of a single solvent-exposed residue enabled the parallel coiled-coil tetramer GCN4-pLI to populate the antiparallel configuration, suggesting that the two configurations are close enough in energy for subtle sequence changes to have important structural consequences. We present a structural analysis of the small changes to the helix register and side-chain conformations that accommodate the two configurations and have supplemented these results using solution studies and a molecular dynamics energetic analysis using a replica exchange methodology. Considering the previous examples of structural nonspecificity in coiled-coil peptides, the findings reported here not only emphasize the predisposition of the coiled-coil motif to adopt multiple configurations but also call attention to the associated risk that observed crytstal structures may not represent the only (or even the major) species present in solution.

Coiled coils at the edge of configurational heterogeneity. Structural analyses of parallel and antiparallel homotetrameric coiled coils reveal configurational sensitivity to a single solvent-exposed amino acid substitution.,Yadav MK, Leman LJ, Price DJ, Brooks CL 3rd, Stout CD, Ghadiri MR Biochemistry. 2006 Apr 11;45(14):4463-73. PMID:16584182^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Yadav MK, Leman LJ, Price DJ, Brooks CL 3rd, Stout CD, Ghadiri MR. Coiled coils at the edge of configurational heterogeneity. Structural analyses of parallel and antiparallel homotetrameric coiled coils reveal configurational sensitivity to a single solvent-exposed amino acid substitution. Biochemistry. 2006 Apr 11;45(14):4463-73. PMID:16584182 doi:10.1021/bi060092q

1 Structural highlights
2 Evolutionary Conservation
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1w5j"

@@ Line 1: / Line 1: @@
 ==AN ANTI-PARALLEL FOUR HELIX BUNDLE==
 <StructureSection load='1w5j' size='340' side='right' caption='[[1w5j]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
@@ Line 5: / Line 6: @@
 </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TYZ:PARA+ACETAMIDO+BENZOIC+ACID'>TYZ</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ce9|1ce9]], [[1dgc|1dgc]], [[1env|1env]], [[1fav|1fav]], [[1gcl|1gcl]], [[1gcm|1gcm]], [[1gk6|1gk6]], [[1gzl|1gzl]], [[1ihq|1ihq]], [[1ij0|1ij0]], [[1ij1|1ij1]], [[1ij2|1ij2]], [[1ij3|1ij3]], [[1kql|1kql]], [[1ld4|1ld4]], [[1llm|1llm]], [[1nkn|1nkn]], [[1piq|1piq]], [[1rb1|1rb1]], [[1rb4|1rb4]], [[1rb5|1rb5]], [[1rb6|1rb6]], [[1swi|1swi]], [[1tmz|1tmz]], [[1m6t|1m6t]], [[1unt|1unt]], [[1unu|1unu]], [[1unv|1unv]], [[1unw|1unw]], [[1unx|1unx]], [[1uny|1uny]], [[1unz|1unz]], [[1uo0|1uo0]], [[1uo1|1uo1]], [[1uo2|1uo2]], [[1uo3|1uo3]], [[1uo4|1uo4]], [[1uo5|1uo5]], [[1vzl|1vzl]], [[1ysa|1ysa]], [[1zii|1zii]], [[1zij|1zij]], [[1zik|1zik]], [[1zil|1zil]], [[1zim|1zim]], [[1zta|1zta]], [[2dgc|2dgc]], [[2zta|2zta]], [[1w5g|1w5g]], [[1w5h|1w5h]], [[1w5i|1w5i]], [[1w5k|1w5k]], [[1w5l|1w5l]]</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1w5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w5j OCA], [http://pdbe.org/1w5j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1w5j RCSB], [http://www.ebi.ac.uk/pdbsum/1w5j PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1w5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w5j OCA], [http://pdbe.org/1w5j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1w5j RCSB], [http://www.ebi.ac.uk/pdbsum/1w5j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1w5j ProSAT]</span></td></tr>
 </table>
 == Evolutionary Conservation ==
@@ Line 11: / Line 12: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/w5/1w5j_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/w5/1w5j_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>

1w5j

From Proteopedia

Revision as of 07:13, 4 April 2018

AN ANTI-PARALLEL FOUR HELIX BUNDLE

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox