1P53

The Crystal Structure of ICAM-1 D3-D5 fragment

• PDB DOI: https://doi.org/10.2210/pdb1P53/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2003-04-24 Released: 2004-05-04 
• Deposition Author(s): Yang, Y., Jun, C.D., Liu, J.H., Zhang, R., Jochimiak, A., Springer, T.A., Wang, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.06 Å
• R-Value Free: 0.252 
• R-Value Work: 0.220 

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

• PubMed: 15099525 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 58.99 kDa 
• Atom Count: 3,955 
• Modelled Residue Count: 500 
• Deposited Residue Count: 532 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Intercellular adhesion molecule-1	A, B	266	Homo sapiens	Mutation(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
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: P05362-1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.06 Å
• R-Value Free: 0.252 
• R-Value Work: 0.220 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 193.7	α = 90
b = 193.7	β = 90
c = 175.3	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
SOLVE	phasing
CCP4	model building
CNS	refinement
HKL-2000	data reduction
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-05-04 
Deposition Author(s): Yang, Y., Jun, C.D., Liu, J.H., Zhang, R., Jochimiak, A., Springer, T.A., Wang, J.H.

Revision History  

• 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