1W5K

AN ANTI-PARALLEL FOUR HELIX BUNDLE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.249 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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, M.K.Leman, L.J.Price, D.J.Brooks, C.L.Stout, C.D.Ghadiri, M.R.

(2006) Biochemistry 45: 4463

  • DOI: 10.1021/bi060092q
  • Primary Citation of Related Structures:  1W5H, 1W5J, 1W5L, 2CCE, 2CCF, 2CCN

  • PubMed Abstract: 
  • 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 ...

    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.


    Organizational Affiliation

    Department of Chemistry, and The Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GENERAL CONTROL PROTEIN GCN4
A, B, C, D
34Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: GCN4 (AAS3, ARG9)
Find proteins for P03069 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P03069
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYZ
Query on TYZ
A, B, C, D
NON-POLYMERC9 H9 N O3

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.249 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 33.886α = 90.00
b = 37.311β = 90.00
c = 104.105γ = 90.00
Software Package:
Software NamePurpose
ARP/wARPphasing
SOLVE/RESOLVEphasing
CrystalCleardata scaling
REFMACrefinement
CrystalCleardata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-09-24
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-06-28
    Type: Refinement description