Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Helical - H  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 6.12 kDa 
• Atom Count: 523 
• Modelled Residue Count: 67 
• Deposited Residue Count: 69 
• Unique protein chains: 1

1Q7D

Structure of the integrin alpha2beta1 binding collagen peptide

• DOI: 10.2210/pdb1Q7D/pdb

• Classification: CONTRACTILE PROTEIN
• Mutation(s): Yes 


• Deposited: 2003-08-18 Released: 2004-01-13 
• Deposition Author(s): Emsley, J., Knight, C.G., Farndale, R.W., Barnes, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.266 
• R-Value Work: 0.236 
• R-Value Observed: 0.236 

Literature

Structure of the Integrin alpha2beta1-binding Collagen Peptide.

Emsley, J., Knight, C.G., Farndale, R.W., Barnes, M.J.

(2004) J Mol Biol 335: 1019-1028

• PubMed: 14698296 
• DOI: 10.1016/j.jmb.2003.11.030
• Primary Citation of Related Structures:  
  1Q7D


• PubMed Abstract: 
  

We have determined the 1.8A crystal structure of a triple helical integrin-binding collagen peptide (IBP) with sequence (Gly-Pro-Hyp)(2)-Gly-Phe-Hyp-Gly-Glu-Arg-(Gly-Pro-Hyp)(3). The central GFOGER hexapeptide is recognised specifically by the integrins alpha2beta1, alpha1beta1, alpha10beta1 and alpha11beta1. These integrin/collagen interactions are implicated in a number of key physiological processes including cell adhesion, cell growth and differentiation, and pathological states such as thrombosis and tumour metastasis. Comparison of the IBP structure with the previously determined structure of an identical collagen peptide in complex with the integrin alpha2-I domain (IBP(c)) allows the first detailed examination of collagen in a bound and an unbound state. The IBP structure shows a direct and a water-mediated electrostatic interaction between Glu and Arg side-chains from adjacent strands, but no intra-strand interactions. The interactions between IBP Glu and Arg side-chains are disrupted upon integrin binding. A comparison of IBP and IBP(c) main-chain conformation reveals the flexible nature of the triple helix backbone in the imino-poor GFOGER region. This flexibility could be important to the integrin-collagen interaction and provides a possible explanation for the unique orientation of the three GFOGER strands observed in the integrin-IBP(c) complex crystal structure.

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Organizational Affiliation: 

Department of Biochemistry, University of Leicester LE17RH, Leicester, UK. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
collagen alfa 1(I) chain peptide GPOGPOGFOGERGPOGPOGPO	A, B, C	23	N/A	Mutation(s): 1
Find proteins for P02452 (Homo sapiens) Explore P02452  Go to UniProtKB:  P02452
NIH Common Fund Data Resources
PHAROS:  P02452 GTEx:  ENSG00000108821

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HYP	A, B, C	L-PEPTIDE LINKING	C5 H9 N O3		PRO

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.266 
• R-Value Work: 0.236 
• R-Value Observed: 0.236 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.6	α = 90
b = 135.8	β = 90
c = 25.4	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-08-18 
• Released Date: 2004-01-13 
Deposition Author(s): Emsley, J., Knight, C.G., Farndale, R.W., Barnes, M.J.

Revision History  

• Version 1.0: 2004-01-13
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance