Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 20.70 kDa 
• Atom Count: 1597 
• Modelled Residue Count: 185 
• Deposited Residue Count: 185 
• Unique protein chains: 1

1IAM

STRUCTURE OF THE TWO AMINO-TERMINAL DOMAINS OF HUMAN INTERCELLULAR ADHESION MOLECULE-1, ICAM-1

• PDB DOI: 10.2210/pdb1IAM/pdb

• Classification: Viral protein receptor
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 1998-02-22 Released: 1998-04-29 
• Deposition Author(s): Bella, J., Kolatkar, P.R., Marlor, C., Greve, J.M., Rossmann, M.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.303 
• R-Value Work: 0.214 
• R-Value Observed: 0.214 

Literature

The structure of the two amino-terminal domains of human ICAM-1 suggests how it functions as a rhinovirus receptor and as an LFA-1 integrin ligand.

Bella, J., Kolatkar, P.R., Marlor, C.W., Greve, J.M., Rossmann, M.G.

(1998) Proc Natl Acad Sci U S A 95: 4140-4145

• PubMed: 9539703 
• DOI: 10.1073/pnas.95.8.4140
• Primary Citation of Related Structures:  
  1IAM


• PubMed Abstract: 
  

The normal function of human intercellular adhesion molecule-1 (ICAM-1) is to provide adhesion between endothelial cells and leukocytes after injury or stress. ICAM-1 binds to leukocyte function-associated antigen (LFA-1) or macrophage-1 antigen (Mac-1). However, ICAM-1 is also used as a receptor by the major group of human rhinoviruses and is a catalyst for the subsequent viral uncoating during cell entry. The three-dimensional atomic structure of the two amino-terminal domains (D1 and D2) of ICAM-1 has been determined to 2.2-A resolution and fitted into a cryoelectron microscopy reconstruction of a rhinovirus-ICAM-1 complex. Rhinovirus attachment is confined to the BC, CD, DE, and FG loops of the amino-terminal Ig-like domain (D1) at the end distal to the cellular membrane. The loops are considerably different in structure to those of human ICAM-2 or murine ICAM-1, which do not bind rhinoviruses. There are extensive charge interactions between ICAM-1 and human rhinoviruses, which are mostly conserved in both major and minor receptor groups of rhinoviruses. The interaction of ICAMs with LFA-1 is known to be mediated by a divalent cation bound to the insertion (I)-domain on the alpha chain of LFA-1 and the carboxyl group of a conserved glutamic acid residue on ICAMs. Domain D1 has been docked with the known structure of the I-domain. The resultant model is consistent with mutational data and provides a structural framework for the adhesion between these molecules.

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Related Citations: 

• Structure of a Human Rhinovirus Complexed with its Receptor Molecule
  Olson, N.H., Kolatkar, P.R., Oliveira, M.A., Cheng, R.H., Greve, J.M., Mcclelland, A., Baker, T.S., Rossmann, M.G.
  (1993) Proc Natl Acad Sci U S A 90: 507

• The Major Human Rhinovirus Receptor is Icam-1
  Greve, J.M., Davis, G., Meyer, A.M., Forte, C.P., Yost, S.C., Marlor, C.W., Kamarck, M.E., Mcclelland, A.
  (1989) Cell 56: 839

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Organizational Affiliation: 

Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-1392, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
INTERCELLULAR ADHESION MOLECULE-1	A	185	Homo sapiens	Mutation(s): 3  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

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.303 
• R-Value Work: 0.214 
• R-Value Observed: 0.214 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.857	α = 90
b = 124.736	β = 90
c = 83.186	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-02-22 
• Released Date: 1998-04-29 
Deposition Author(s): Bella, J., Kolatkar, P.R., Marlor, C., Greve, J.M., Rossmann, M.G.

Revision History  

• Version 1.0: 1998-04-29
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.5: 2021-11-03
  Changes: Database references, Structure summary