3T4F

Crystal Structure of a KGE Collagen Mimetic Peptide at 1.68 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.141 
  • R-Value Work: 0.101 
  • R-Value Observed: 0.103 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Structural insights into charge pair interactions in triple helical collagen-like proteins.

Fallas, J.A.Dong, J.Tao, Y.J.Hartgerink, J.D.

(2012) J Biol Chem 287: 8039-8047

  • DOI: https://doi.org/10.1074/jbc.M111.296574
  • Primary Citation of Related Structures:  
    3T4F, 3U29

  • PubMed Abstract: 

    The collagen triple helix is the most abundant protein fold in humans. Despite its deceptively simple structure, very little is understood about its folding and fibrillization energy landscape. In this work, using a combination of x-ray crystallography and nuclear magnetic resonance spectroscopy, we carry out a detailed study of stabilizing pair-wise interactions between the positively charged lysine and the negatively charged amino acids aspartate and glutamate. We find important differences in the side chain conformation of amino acids in the crystalline and solution state. Structures from x-ray crystallography may have similarities to the densely packed triple helices of collagen fibers whereas solution NMR structures reveal the simpler interactions of isolated triple helices. In solution, two distinct types of contacts are observed: axial and lateral. Such register-specific interactions are crucial for the understanding of the registration process of collagens and the overall stability of proteins in this family. However, in the crystalline state, there is a significant rearrangement of the side chain conformation allowing for packing interactions between adjacent helices, which suggests that charged amino acids may play a dual role in collagen stabilization and folding, first at the level of triple helical assembly and second during fibril formation.


  • Organizational Affiliation

    Department of Chemistry, Rice University, Houston, Texas 77005, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
collagen mimetic peptide
A, B, C, D, E
A, B, C, D, E, F
26synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
HYP
Query on HYP
A, B, C, D, E
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H9 N O3PRO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.141 
  • R-Value Work: 0.101 
  • R-Value Observed: 0.103 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 14.026α = 95.01
b = 23.815β = 94.69
c = 67.657γ = 94.86
Software Package:
Software NamePurpose
PHENIXrefinement
CrystalCleardata collection
EPMRphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesDMR-0645474
Robert A. Welch FoundationUnited StatesC1557
Robert A. Welch FoundationUnited StatesC1565

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-28
    Type: Initial release
  • Version 1.1: 2012-05-09
    Changes: Database references
  • Version 2.0: 2020-09-02
    Type: Coordinate replacement
    Reason: Sequence discrepancy
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2023-09-13
    Changes: Data collection, Database references, Refinement description