1P53

The Crystal Structure of ICAM-1 D3-D5 fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free: 
    0.252 (Depositor), 0.251 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.222 (DCC) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 2.1 of the entry. See complete history


Literature

Structural basis for dimerization of ICAM-1 on the cell surface.

Yang, Y.Jun, C.D.Liu, J.H.Zhang, R.Joachimiak, A.Springer, T.A.Wang, J.H.

(2004) Mol Cell 14: 269-276

  • DOI: https://doi.org/10.1016/s1097-2765(04)00204-7
  • Primary Citation of Related Structures:  
    1P53

  • PubMed Abstract: 

    We have determined the 3.0 A crystal structure of the three C-terminal domains 3-5 (D3-D5) of ICAM-1. Combined with the previously known N-terminal two-domain structure (D1D2), a model of an entire ICAM-1 extracellular fragment has been constructed. This model should represent a general architecture of other ICAM family members, particularly ICAM-3 and ICAM-5. The observed intimate dimerization interaction at D4 and a stiff D4-D5 stem-like architecture provide a good structural explanation for the existence of preformed ICAM-1 cis dimers on the cell membrane. Together with another dimerization interface at D1, a band-like one-dimensional linear cluster of ICAM-1 on an antigen-presenting cell (APC) surface can be envisioned, which might explain the formation of an immunological synapse between an activated T cell and APC which is critical for T cell receptor signaling.


  • Organizational Affiliation

    Dana-Farber Cancer Institute, Boston, MA 02115, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Intercellular adhesion molecule-1
A, B
266Homo sapiensMutation(s): 0 
Gene Names: ICAM1
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: 3Go to GlyGen: P05362-1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free:  0.252 (Depositor), 0.251 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.222 (DCC) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 193.7α = 90
b = 193.7β = 90
c = 175.3γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CCP4model building
CNSrefinement
HKL-2000data reduction
CCP4phasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-05-04
    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 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-10-09
    Changes: Data collection, Database references, Structure summary