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- PDB-1d3l: D1D2-ICAM-1 FULLY GLYCOSYLATED, VARIATION OF D1-D2 INTERDOMAIN AN... -

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Basic information

Entry
Database: PDB / ID: 1d3l
TitleD1D2-ICAM-1 FULLY GLYCOSYLATED, VARIATION OF D1-D2 INTERDOMAIN ANGLE IN DIFFERENT CRYSTAL STRUCTURES.
ComponentsPROTEIN (INTERCELLULAR ADHESION MOLECULE-1)
KeywordsCELL ADHESION / RHINOVIRUS RECEPTOR / ADHESION PROTEIN / GLYCOPROTEIN / IMMUNOGLOBULIN FOLD
Function / homology
Function and homology information


regulation of leukocyte mediated cytotoxicity / T cell extravasation / positive regulation of cellular extravasation / regulation of ruffle assembly / T cell antigen processing and presentation / membrane to membrane docking / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / adhesion of symbiont to host / establishment of endothelial barrier / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules ...regulation of leukocyte mediated cytotoxicity / T cell extravasation / positive regulation of cellular extravasation / regulation of ruffle assembly / T cell antigen processing and presentation / membrane to membrane docking / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / adhesion of symbiont to host / establishment of endothelial barrier / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte migration / leukocyte cell-cell adhesion / cell adhesion mediated by integrin / Interleukin-10 signaling / immunological synapse / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / cellular response to leukemia inhibitory factor / cellular response to glucose stimulus / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / cellular response to amyloid-beta / integrin binding / transmembrane signaling receptor activity / signaling receptor activity / virus receptor activity / : / Interleukin-4 and Interleukin-13 signaling / receptor-mediated virion attachment to host cell / positive regulation of ERK1 and ERK2 cascade / cell adhesion / membrane raft / external side of plasma membrane / focal adhesion / cell surface / extracellular space / extracellular exosome / membrane / plasma membrane
Similarity search - Function
: / ICAM-1/3/5, D2 domain / Intercellular adhesion molecule / Intercellular adhesion molecule, N-terminal / Intercellular adhesion molecule (ICAM), N-terminal domain / Intercellular adhesion molecule/vascular cell adhesion molecule, N-terminal / : / Immunoglobulin domain / Immunoglobulin subtype / Immunoglobulin ...: / ICAM-1/3/5, D2 domain / Intercellular adhesion molecule / Intercellular adhesion molecule, N-terminal / Intercellular adhesion molecule (ICAM), N-terminal domain / Intercellular adhesion molecule/vascular cell adhesion molecule, N-terminal / : / Immunoglobulin domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Intercellular adhesion molecule 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsBella, J. / Kolatkar, P.R. / Rossmann, M.G.
Citation
Journal: EMBO J / Year: 1999
Title: Structural studies of two rhinovirus serotypes complexed with fragments of their cellular receptor.
Authors: P R Kolatkar / J Bella / N H Olson / C M Bator / T S Baker / M G Rossmann /
Abstract: Two human rhinovirus serotypes complexed with two- and five-domain soluble fragments of the cellular receptor, intercellular adhesion molecule-1, have been investigated by X-ray crystallographic ...Two human rhinovirus serotypes complexed with two- and five-domain soluble fragments of the cellular receptor, intercellular adhesion molecule-1, have been investigated by X-ray crystallographic analyses of the individual components and by cryo-electron microscopy of the complexes. The three-dimensional image reconstructions provide a molecular envelope within which the crystal structures of the viruses and the receptor fragments can be positioned with accuracy. The N-terminal domain of the receptor binds to the rhinovirus 'canyon' surrounding the icosahedral 5-fold axes. Fitting of molecular models into the image reconstruction density identified the residues on the virus that interact with those on the receptor surface, demonstrating complementarity of the electrostatic patterns for the tip of the N-terminal receptor domain and the floor of the canyon. The complexes seen in the image reconstructions probably represent the first stage of a multistep binding process. A mechanism is proposed for the subsequent viral uncoating process.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: 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.
Authors: Bella, J. / Kolatkar, P.R. / Marlor, C.W. / Greve, J.M. / Rossmann, M.G.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: A Dimeric Crystal Structure for the N-Terminal Two Domains of Intercellular Adhesion Molecule-1
Authors: Casasnovas, J.M. / Stehle, T. / Liu, J.H. / Wang, J.H. / Springer, T.A.
#3: Journal: J.Mol.Biol. / Year: 1992
Title: Preliminary X-Ray Crystallographic Analysis of Intercellular Adhesion Molecule-1
Authors: Kolatkar, P.R. / Oliveira, M.A. / Rossmann, M.G. / Robbins, A.H. / Katti, S. / Hoover-Litty, H. / Forte, C. / Greve, J.M. / Mcclelland, A. / Olson, N.H.
History
DepositionSep 29, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (INTERCELLULAR ADHESION MOLECULE-1)


Theoretical massNumber of molelcules
Total (without water)20,4381
Polymers20,4381
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.070, 54.070, 145.770
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PROTEIN (INTERCELLULAR ADHESION MOLECULE-1) / ICAM-1 / Coordinate model: Cα atoms only


Mass: 20438.260 Da / Num. of mol.: 1 / Fragment: FIRST TWO DOMAINS, RESIDUES 1-185 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05362

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.1 %
Crystal growDetails: PROTEIN WAS DESIALATED WITH NEURAMINIDASE (8 HR AT 37 DEGREES IN 100 MM SODIUM ACETATE, PH 6.5, 10 MG/ML PROTEIN, 0.1 ENZYME UNIT/ML), DIALYZED AGAINST 10 MM TRIS, 25 MM NACL (PH 6.0), AND ...Details: PROTEIN WAS DESIALATED WITH NEURAMINIDASE (8 HR AT 37 DEGREES IN 100 MM SODIUM ACETATE, PH 6.5, 10 MG/ML PROTEIN, 0.1 ENZYME UNIT/ML), DIALYZED AGAINST 10 MM TRIS, 25 MM NACL (PH 6.0), AND PASSED THROUGH MONO-Q COLUMN. DESIALATED MATERIAL WAS CRYSTALLIZED BY HANGING DROP METHODS: 17 MG/ML PROTEIN IN BUFFER: 10 MM TRIS,25 MM NACL,1 MM MGCL2,1 MM CACL2, WAS PRECIPITATED FROM 24-27% PEG 3350 IN SAME BUFFER.
Crystal grow
*PLUS
Method: other / Details: Kolatkar, P.R., (1992) J. Mol. Biol., 225, 1127.

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.816→26.582 Å / Num. obs: 4634 / % possible obs: 72.1 %
Reflection shellResolution: 2.82→2.94 Å / % possible all: 21.8

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Processing

SoftwareName: AMoRE / Classification: phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IAM

1iam


Resolution: 3.25→15 Å / σ(F): 0 / Details: COORDINATES AFTER RIGID-BODY REFINEMENT
RfactorNum. reflection% reflection
Rwork0.371 --
obs-3841 91.8 %
Displacement parametersBiso mean: 41.89 Å2
Refinement stepCycle: LAST / Resolution: 3.25→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms185 0 0 0 185

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