1CK4 | pdb_00001ck4

CRYSTAL STRUCTURE OF RAT A1B1 INTEGRIN I-DOMAIN.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.299 (Depositor), 0.302 (DCC) 
  • R-Value Work: 
    0.234 (Depositor), 0.226 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the alpha1beta1 integrin I-domain: insights into integrin I-domain function.

Nolte, M.Pepinsky, R.B.Venyaminov, S.Y.u.Koteliansky, V.Gotwals, P.J.Karpusas, M.

(1999) FEBS Lett 452: 379-385

  • DOI: https://doi.org/10.1016/s0014-5793(99)00666-3
  • Primary Citation Related Structures: 
    1CK4

  • PubMed Abstract: 

    The alpha1beta1 integrin is a major cell surface receptor for collagen. Ligand binding is mediated, in part, through a 200 amino acid inserted 'I'-domain contained in the extracellular part of the integrin alpha chain. Integrin I-domains contain a divalent cation binding (MIDAS) site and require cations to interact with integrin ligands. We have determined the crystal structure of recombinant I-domain from the rat alpha1beta1 integrin at 2.2 A resolution in the absence of divalent cations. The alpha1 I-domain adopts the dinucleotide binding fold that is characteristic of all I-domain structures that have been solved to date and has a structure very similar to that of the closely related alpha2beta1 I-domain which also mediates collagen binding. A unique feature of the alpha1 I-domain crystal structure is that the MIDAS site is occupied by an arginine side chain from another I-domain molecule in the crystal, in place of a metal ion. This interaction supports a proposed model for ligand-induced displacement of metal ions. Circular dichroism spectra determined in the presence of Ca2+, Mg2+ and Mn2+ indicate that no changes in the structure of the I-domain occur upon metal ion binding in solution. Metal ion binding induces small changes in UV absorption spectra, indicating a change in the polarity of the MIDAS site environment.


  • Organizational Affiliation
    • Biogen, Inc., Cambridge, MA 02142, USA.

Macromolecule Content 

  • Total Structure Weight: 44.24 kDa 
  • Atom Count: 3,258 
  • Modeled Residue Count: 388 
  • Deposited Residue Count: 396 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
INTEGRIN ALPHA-1
A, B
198Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P18614 (Rattus norvegicus)
Explore P18614 
Go to UniProtKB:  P18614
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18614
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.299 (Depositor), 0.302 (DCC) 
  • R-Value Work:  0.234 (Depositor), 0.226 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.77α = 90
b = 85.92β = 90
c = 132.56γ = 90
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-05-03
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-09
    Changes: Data collection, Database references, Refinement description