1EI8

STRUCTURAL CONSEQUENCES OF A DISCONTINUITY IN THE REPEATING TRIPEPTIDE SEQUENCE OF A COLLAGEN-LIKE TRIPLE-HELICAL PEPTIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Conformational effects of gly-x-gly interruptions in the collagen triple helix.

Bella, J.Liu, J.Kramer, R.Brodsky, B.Berman, H.M.

(2006) J.Mol.Biol. 362: 298-311

  • DOI: 10.1016/j.jmb.2006.07.014

  • PubMed Abstract: 
  • The collagen model peptide with sequence (Pro-Hyp-Gly)4-Pro-Gly-(Pro-Hyp-Gly)5 contains a central Gly-Pro-Gly interruption in the consensus collagen sequence. Its high-resolution crystal structure defines the molecular consequences of such an interru ...

    The collagen model peptide with sequence (Pro-Hyp-Gly)4-Pro-Gly-(Pro-Hyp-Gly)5 contains a central Gly-Pro-Gly interruption in the consensus collagen sequence. Its high-resolution crystal structure defines the molecular consequences of such an interruption for the collagen triple-helical conformation, and provides insight into possible structural and biological roles of similar interruptions in the -Gly-X-Y- repeating pattern found in non-fibrillar collagens. The peptide (denoted as the Hyp minus peptide or Hyp-) forms a rod-like triple helix structure without any bend or kink, and crystallizes in a quasi-hexagonal lattice. The two Pro-Hyp-Gly zones adopt the typical triple-helical collagen conformation with standard Rich and Crick II hydrogen bonding topology. Notably, the central zone containing the Gly-Pro-Gly interruption deviates from the standard structure in terms of hydrogen bonding topology, torsion angles, helical, and superhelical parameters. These deviations are highly localized, such that the standard features are regained within one to two residues on either side. Conformational variations and high temperature factors seen for the six chains of the asymmetric unit in the zone around the interruption point to the presence of a local region of considerable plasticity and flexibility embedded within two highly rigid and ordered standard triple-helical segments. The structure suggests a role for Gly-X-Gly interruptions as defining regions of flexibility and molecular recognition in the otherwise relatively uniform repeating collagen conformation.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
COLLAGEN-LIKE PEPTIDE (PRO-HYP-GLY)4-PG-(PRO-HYP-GLY)5
A, B, C, D, E, F
29Drosophila melanogasterN/A
Find proteins for Q8T018 (Drosophila melanogaster)
Go to UniProtKB:  Q8T018
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
HYP
Query on HYP
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H9 N O3PRO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.217 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 14.150α = 85.86
b = 23.770β = 85.54
c = 82.210γ = 84.34
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2000-02-24 
  • Released Date: 2003-09-09 
  • Deposition Author(s): Berman, H.M., Liu, J.

Revision History 

  • Version 1.0: 2003-09-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance