I domain from human integrin alpha1-beta1

Experimental Data Snapshot

  • Resolution: 1.87 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Jararhagin-derived RKKH peptides induce structural changes in alpha1I domain of human integrin alpha1beta1.

Nymalm, Y.Puranen, J.S.Nyholm, T.K.M.Kapyla, J.Kidron, H.Airenne, T.T.Heino, J.Slotte, J.P.Johnson, M.S.Salminen, T.A.

(2004) J Biol Chem 279: 7962-7970

  • DOI: https://doi.org/10.1074/jbc.M312912200
  • Primary Citation of Related Structures:  
    1PT6, 1QCY

  • PubMed Abstract: 

    Integrin alpha(1)beta(1) is one of four collagen-binding integrins in humans. Collagens bind to the alphaI domain and in the case of alpha(2)I collagen binding is competitively inhibited by peptides containing the RKKH sequence and derived from the metalloproteinase jararhagin of snake venom from Bothrops jararaca. In alpha(2)I, these peptides bind near the metal ion-dependent adhesion site (MIDAS), where a collagen (I)-like peptide is known to bind; magnesium is required for binding. Published structures of the ligand-bound "open" conformation of alpha(2)I differs significantly from the "closed" conformation seen in the structure of apo-alpha(2)I near MIDAS. Here we show that two peptides, CTRKKHDC and CARKKHDC, derived from jararhagin also bind to alpha(1)I and competitively inhibit collagen I binding. Furthermore, calorimetric and fluorimetric measurements show that the structure of the complex of alpha(1)I with Mg(2+) and CTRKKHDC differs from structure in the absence of peptide. A comparison of the x-ray structure of apo-alpha(1)I ("closed" conformation) and a model structure of the alpha(1)I ("open" conformation) based on the closely related structure of alpha(2)I reveals that the binding site is partially blocked to ligands by Glu(255) and Tyr(285) in the "closed" structure, whereas in the "open" structure helix C is unwound and these residues are shifted, and the "RKKH" peptides fit well when docked. The "open" conformation of alpha(2)I resulting from binding a collagen (I)-like peptide leads to exposure of hydrophobic surface, also seen in the model of alpha(1)I and shown experimentally for alpha(1)I using a fluorescent hydrophobic probe.

  • Organizational Affiliation

    Department of Biochemistry and Pharmacy, Abo Akademi University, P.O. Box 66, FIN-20521, Turku, Finland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Integrin alpha-1
A, B
213Homo sapiensMutation(s): 0 
Gene Names: ITGA1
UniProt & NIH Common Fund Data Resources
Find proteins for P56199 (Homo sapiens)
Explore P56199 
Go to UniProtKB:  P56199
PHAROS:  P56199
GTEx:  ENSG00000213949 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56199
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.87 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.471α = 90
b = 97.601β = 103.63
c = 53.094γ = 90
Software Package:
Software NamePurpose
MAR345data collection
XDSdata scaling

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-04-13
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description