1MQ8 | pdb_00001mq8

Crystal structure of alphaL I domain in complex with ICAM-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 
    0.313 (Depositor) 
  • R-Value Work: 
    0.264 (Depositor), 0.256 (DCC) 
  • R-Value Observed: 
    0.280 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history

Literature

Structures of the aL I domain and its complex with ICAM-1 reveal a shape-shifting pathway for integrin regulation

Shimaoka, M.Xiao, T.Liu, J.-H.Yang, Y.Dong, Y.Jun, C.-D.McCormack, A.Zhang, R.Joachimiak, A.Takagi, J.Wang, J.-H.Springer, T.A.

(2003) Cell 112: 99-111

  • DOI: https://doi.org/10.1016/s0092-8674(02)01257-6
  • Primary Citation Related Structures: 
    1MJN, 1MQ8, 1MQ9, 1MQA

  • PubMed Abstract: 

    The structure of the I domain of integrin alpha L beta 2 bound to the Ig superfamily ligand ICAM-1 reveals the open ligand binding conformation and the first example of an integrin-IgSF interface. The I domain Mg2+ directly coordinates Glu-34 of ICAM-1, and a dramatic swing of I domain residue Glu-241 enables a critical salt bridge. Liganded and unliganded structures for both high- and intermediate-affinity mutant I domains reveal that ligand binding can induce conformational change in the alpha L I domain and that allosteric signals can convert the closed conformation to intermediate or open conformations without ligand binding. Pulling down on the C-terminal alpha 7 helix with introduced disulfide bonds ratchets the beta 6-alpha 7 loop into three different positions in the closed, intermediate, and open conformations, with a progressive increase in affinity.


  • Organizational Affiliation
    • The Center for Blood Research, Department of Pathology, Department of Anesthesia, Department of Pediatrics, Boston, Massachusetts 02115.

Macromolecule Content 

  • Total Structure Weight: 106.26 kDa 
  • Atom Count: 5,854 
  • Modeled Residue Count: 722 
  • Deposited Residue Count: 936 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
intercellular adhesion molecule-1
A, C
291Homo sapiensMutation(s): 0 
Gene Names: ICAM-1
UniProt & NIH Common Fund Data Resources
Find proteins for P05362 (Homo sapiens)
Explore P05362 
Go to UniProtKB:  P05362
PHAROS:  P05362
GTEx:  ENSG00000090339 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05362
Glycosylation
Glycosylation Sites: 4Go to GlyGen: P05362-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Integrin alpha-L
B, D
177Homo sapiensMutation(s): 2 
Gene Names: LFA-1 (AlphaLbeta2)
UniProt & NIH Common Fund Data Resources
Find proteins for P20701 (Homo sapiens)
Explore P20701 
Go to UniProtKB:  P20701
PHAROS:  P20701
GTEx:  ENSG00000005844 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20701
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, F, G, H
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free:  0.313 (Depositor) 
  • R-Value Work:  0.264 (Depositor), 0.256 (DCC) 
  • R-Value Observed: 0.280 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.56α = 95.39
b = 62.868β = 106.67
c = 81.517γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-01-14
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2021-10-27
    Changes: Database references, Structure summary
  • Version 2.2: 2024-11-13
    Changes: Data collection, Refinement description, Structure summary