Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 21.57 kDa 
• Atom Count: 1609 
• Residue Count: 193 
• Unique protein chains: 1

1QCY

THE CRYSTAL STRUCTURE OF THE I-DOMAIN OF HUMAN INTEGRIN ALPHA1BETA1

• DOI: 10.2210/pdb1QCY/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-05-12 Released: 2003-09-02 
• Deposition Author(s): Kankare, J.A., Salminen, T.A., Nymalm, Y., Kaepylae, J., Heino, J., Johnson, M.S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.258 
• R-Value Work: 0.200 

Literature

Jararhagin-derived RKKH Peptides Induce Structural Changes in a1I Domain of Human Integrin a1b1

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

(2004) J Biol Chem 279: 7962-7970

• PubMed: 14660600 
• DOI: 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.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
I-DOMAIN OF INTEGRIN ALPHA1BETA1	A	193	Homo sapiens	Mutation(s): 0  Gene Names: ITGA1
Find proteins for P56199 (Homo sapiens) Explore P56199  Go to UniProtKB:  P56199
NIH Common Fund Data Resources
PHAROS:  P56199 GTEx:  ENSG00000213949

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.258 
• R-Value Work: 0.200 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.457	α = 90
b = 81.858	β = 90.78
c = 37.316	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-05-12 
• Released Date: 2003-09-02 
Deposition Author(s): Kankare, J.A., Salminen, T.A., Nymalm, Y., Kaepylae, J., Heino, J., Johnson, M.S.

Revision History 

• Version 1.0: 2003-09-02
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2014-11-12
  Changes: Structure summary