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- PDB-1iam: STRUCTURE OF THE TWO AMINO-TERMINAL DOMAINS OF HUMAN INTERCELLULA... -

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Entry
Database: PDB / ID: 1iam
TitleSTRUCTURE OF THE TWO AMINO-TERMINAL DOMAINS OF HUMAN INTERCELLULAR ADHESION MOLECULE-1, ICAM-1
ComponentsINTERCELLULAR ADHESION MOLECULE-1
KeywordsViral protein receptor / RHINOVIRUS RECEPTOR / CELL ADHESION / INTEGRIN LIGAND / GLYCOPROTEIN / LFA-1 LIGAND / IMMUNOGLOBULIN FOLD / TRANSMEMBRANE
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 / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / membrane to membrane docking / adhesion of symbiont to host / establishment of endothelial barrier / cell adhesion mediated by integrin ...regulation of leukocyte mediated cytotoxicity / T cell extravasation / positive regulation of cellular extravasation / regulation of ruffle assembly / T cell antigen processing and presentation / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / membrane to membrane docking / adhesion of symbiont to host / establishment of endothelial barrier / cell adhesion mediated by integrin / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / leukocyte migration / 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 / cellular response to amyloid-beta / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / transmembrane signaling receptor activity / integrin binding / virus receptor activity / signaling receptor activity / collagen-containing extracellular matrix / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Intercellular adhesion molecule 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, MIR, PHASE RECOMBINATION / Resolution: 2.1 Å
AuthorsBella, J. / Kolatkar, P.R. / Marlor, C. / Greve, J.M. / Rossmann, M.G.
Citation
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.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Structure of a Human Rhinovirus Complexed with its Receptor Molecule
Authors: Olson, N.H. / Kolatkar, P.R. / Oliveira, M.A. / Cheng, R.H. / Greve, J.M. / Mcclelland, A. / Baker, T.S. / Rossmann, M.G.
#2: Journal: Cell(Cambridge,Mass.) / Year: 1989
Title: The Major Human Rhinovirus Receptor is Icam-1
Authors: Greve, J.M. / Davis, G. / Meyer, A.M. / Forte, C.P. / Yost, S.C. / Marlor, C.W. / Kamarck, M.E. / Mcclelland, A.
History
DepositionFeb 22, 1998Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Nov 3, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTERCELLULAR ADHESION MOLECULE-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7022
Polymers20,4801
Non-polymers2211
Water2,648147
1
A: INTERCELLULAR ADHESION MOLECULE-1
hetero molecules

A: INTERCELLULAR ADHESION MOLECULE-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4034
Polymers40,9612
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Unit cell
Length a, b, c (Å)41.857, 124.736, 83.186
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-514-

HOH

21A-515-

HOH

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Components

#1: Protein INTERCELLULAR ADHESION MOLECULE-1 / / ICAM-1 / CD54


Mass: 20480.338 Da / Num. of mol.: 1 / Fragment: TWO N-TERMINAL, IMMUNOGLOBULIN DOMAINS / Mutation: N103Q, N118Q, N156Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: LEUKOCYTES, ENDOTHELIAL CELLS / Cell line: SF9 / Plasmid: PVL1393 (PHARMINGEN) / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P05362
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.56 %
Description: THERE IS A SIGNIFICANT NUMBER OF OVERLOADS IN THE LOWER RESOLUTION SHELLS (19% BETWEEN 20 AN 5 ANGSTROM). DATA WAS SCALED WITH THE "INCLUDE OVERLOADS" OPTION IN SCALEPACK. LOW RESOLUTION ...Description: THERE IS A SIGNIFICANT NUMBER OF OVERLOADS IN THE LOWER RESOLUTION SHELLS (19% BETWEEN 20 AN 5 ANGSTROM). DATA WAS SCALED WITH THE "INCLUDE OVERLOADS" OPTION IN SCALEPACK. LOW RESOLUTION DATA BETWEEN 20 AND 5 ANGSTROM HAS NOT BEEN USED IN THE REFINEMENT.
Crystal growpH: 7.5
Details: PROTEIN IN 10 MM TRIS, PH 7.5, 25 MM NACL, WAS CRYSTALLIZED FROM 20% PEG 4000 IN 10 MM TRIS AS PRECIPITANT
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
210 mMTris1drop
325 mM1dropNaCl
420 %PEG40001reservoir
510 mMTris1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.92
DetectorDetector: CCD / Date: Feb 26, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 10629 / % possible obs: 81.1 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 24.15
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 0.3 % / Rmerge(I) obs: 0.059 / Mean I/σ(I) obs: 10.21 / % possible all: 33.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, MIR, PHASE RECOMBINATION
Starting model: ICAM-2, PDB ENTRY 1ZXQ

1zxq


Resolution: 2.1→5 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.303 971 10.1 %RANDOM
Rwork0.214 ---
obs0.214 9599 79.5 %-
Displacement parametersBiso mean: 24.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.7699 Å20 Å20 Å2
2---0.906 Å20 Å2
3----2.8639 Å2
Refinement stepCycle: LAST / Resolution: 2.1→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1436 0 14 147 1597
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.6
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.271.5
X-RAY DIFFRACTIONx_mcangle_it1.812
X-RAY DIFFRACTIONx_scbond_it2.122
X-RAY DIFFRACTIONx_scangle_it2.712.5
LS refinement shellResolution: 2.1→2.19 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.242 43 9.91 %
Rwork0.219 331 -
obs--29 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM3.CHOTOPH3.CHO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.6

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