1MHP

Crystal structure of a chimeric alpha1 integrin I-domain in complex with the Fab fragment of a humanized neutralizing antibody

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.222 

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This is version 1.2 of the entry. See complete history. 


Literature

Crystal Structure of the alpha 1 beta 1 Integrin I Domain in Complex with an Antibody Fab Fragment

Karpusas, M., Ferrant, J., Weinreb, P., Carmillo, A., Taylor, F., Garber, E.

(2003) J Mol Biol 327: 1031-1041

  • DOI: 10.1016/s0022-2836(03)00203-1
  • Primary Citation of Related Structures:  
    1MHP

  • PubMed Abstract: 

    • The alpha1beta1 (VLA-1) integrin is a cell-surface receptor for collagen and laminin and has been implicated in biological pathways involved in several pathological processes. These processes may be inhibited by the monoclonal antibody AQC2, which binds ...

    The alpha1beta1 (VLA-1) integrin is a cell-surface receptor for collagen and laminin and has been implicated in biological pathways involved in several pathological processes. These processes may be inhibited by the monoclonal antibody AQC2, which binds with high affinity to human alpha1beta1 integrin. To understand the structural basis of the inhibition we determined the crystal structure of the complex of a chimeric rat/human I domain of the alpha1beta1 integrin and the Fab fragment of humanized AQC2 antibody. The structure of the complex shows that the antibody blocks the collagen binding site of the I domain. An aspartate residue, from the CDR3 loop of the antibody heavy chain, coordinates the MIDAS metal ion in a manner similar to that of a glutamate residue from collagen. Substitution of the aspartate residue by alanine or arginine results in significant reduction of antibody binding affinity. Interestingly, although the mode of metal ion coordination resembles that of the open conformation, the I domain maintains an overall closed conformation previously observed only for unliganded I domains.

    Organizational Affiliation: 

    Biogen, Inc., 14 Cambridge Center, Cambridge, MA 02142, USA. michael_karpusas@yahoo.com



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
integrin alpha 1, (RESIDUES 169-360) A, B192Rattus norvegicusMutation(s): 4 
Gene Names: Itga1
Find proteins for P18614 (Rattus norvegicus)
Explore P18614 
Go to UniProtKB:  P18614
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fab fragment, heavy chain H, X219Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
FAB FRAGMENT, light chain L, Y212Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN
Download Ideal Coordinates CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.222 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 255.09α = 90
b = 255.09β = 90
c = 38.64γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-04-15
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance