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- PDB-1zxq: THE CRYSTAL STRUCTURE OF ICAM-2 -

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Basic information

Entry
Database: PDB / ID: 1zxq
TitleTHE CRYSTAL STRUCTURE OF ICAM-2
ComponentsINTERCELLULAR ADHESION MOLECULE-2
KeywordsCELL ADHESION / IMMUNOGLOBULIN FOLD / GLYCOPROTEIN / TRANSMEMBRANE
Function / homology
Function and homology information


uropod / plasma membrane => GO:0005886 / stimulatory C-type lectin receptor signaling pathway / microvillus / cleavage furrow / regulation of immune response / Integrin cell surface interactions / CD209 (DC-SIGN) signaling / extracellular matrix organization / cell-cell adhesion ...uropod / plasma membrane => GO:0005886 / stimulatory C-type lectin receptor signaling pathway / microvillus / cleavage furrow / regulation of immune response / Integrin cell surface interactions / CD209 (DC-SIGN) signaling / extracellular matrix organization / cell-cell adhesion / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / cell adhesion / membrane / plasma membrane
Similarity search - Function
Intercellular adhesion molecule 2 / 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-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Intercellular adhesion molecule 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.2 Å
AuthorsCasasnovas, J.M. / Springer, T.A. / Harrison, S.C. / Wang, J.-H.
CitationJournal: Nature / Year: 1997
Title: Crystal structure of ICAM-2 reveals a distinctive integrin recognition surface.
Authors: Casasnovas, J.M. / Springer, T.A. / Liu, J.H. / Harrison, S.C. / Wang, J.H.
History
DepositionMar 4, 1997Processing site: BNL
Revision 1.0Sep 4, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INTERCELLULAR ADHESION MOLECULE-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9317
Polymers21,3841
Non-polymers2,5466
Water2,558142
1
A: INTERCELLULAR ADHESION MOLECULE-2
hetero molecules

A: INTERCELLULAR ADHESION MOLECULE-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,86114
Polymers42,7692
Non-polymers5,09312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Unit cell
Length a, b, c (Å)69.000, 63.700, 76.200
Angle α, β, γ (deg.)90.00, 114.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein INTERCELLULAR ADHESION MOLECULE-2 / ICAM-2


Mass: 21384.320 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR REGION WITH THE TWO IG-LIKE DOMAINS
Source method: isolated from a genetically manipulated source
Details: THE SIXTH INTERNATIONAL WORKSHOP ON HUMAN LEUKOCYTE DIFFERENTIATION ANTIGENS NUMBER CD102
Source: (gene. exp.) Homo sapiens (human) / Cell: HEMATOPOIETIC AND ENDOTHELIAL CELLS / Gene: ICAM-2 / Organ: OVARY / Plasmid: PBJ5-GS/ICAM-2
Cell line (production host): CHINESE HAMSTER OVARY CELLS (CHO)
Gene (production host): ICAM-2 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P13598
#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Compound detailsINTERCELLULAR ADHESION MOLECULE 2 (ICAM-2) IS ONE OF THREE KNOWN MEMBERS OF ICAM SUBFAMILY OF ...INTERCELLULAR ADHESION MOLECULE 2 (ICAM-2) IS ONE OF THREE KNOWN MEMBERS OF ICAM SUBFAMILY OF ADHESION RECEPTORS (ICAM-1, -2, AND -3). IT BINDS TO THE INTEGRIN LYMPHOCYTE FUNCTION-ASSOCIATED ANTIGEN (LFA-1) AND MEDIATES ADHESIVE INTERACTIONS IMPORTANT FOR ANTIGEN-SPECIFIC IMMUNE RESPONSE, NK-CELL MEDIATED CLEARANCE, LYMPHOCYTE RECIRCULATION, AND OTHER CELLULAR INTERACTIONS IMPORTANT FOR IMMUNE RESPONSE AND SURVEILLANCE.

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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: 3.56 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: CRYSTALS WERE BEST GROWN AT 4C USING THE HANGING-DROP VAPOR DIFFUSION METHOD, WITH A PROTEIN SOLUTION OF 15-17 MG/ML AND A CRYSTALLIZATION SOLUTION WITH 20% PEG 4000, 20 MM CACODYLATE BUFFER ...Details: CRYSTALS WERE BEST GROWN AT 4C USING THE HANGING-DROP VAPOR DIFFUSION METHOD, WITH A PROTEIN SOLUTION OF 15-17 MG/ML AND A CRYSTALLIZATION SOLUTION WITH 20% PEG 4000, 20 MM CACODYLATE BUFFER PH 6.4, AND 25 MM B-OCTYL-GLUCOPYRANOSIDE., vapor diffusion - hanging drop, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115-17 mg/mlprotein1drop
220 %PEG40001reservoir
320 mMcacodylate1reservoir
425 mMbeta-octyl glucopyranoside1reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Apr 20, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→100 Å / Num. obs: 14277 / % possible obs: 93.9 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.44 / Net I/σ(I): 10.5
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.141 / Mean I/σ(I) obs: 4.2 / % possible all: 68.8
Reflection shell
*PLUS
% possible obs: 68.8 %

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Processing

Software
NameVersionClassification
XDSdata scaling
CCP4data reduction
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2.2→15 Å / σ(F): 2
Details: SOLVENT CORRECTION. ANISOTROPIC B-FACTOR CORRECTION APPLIED TO FO.
Rfactor% reflection
Rfree0.295 10 %
Rwork0.226 -
obs0.226 88.3 %
Displacement parametersBiso mean: 50 Å2
Baniso -1Baniso -2Baniso -3
1-12.8 Å20 Å210.9 Å2
2--17.4 Å20 Å2
3---26.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1500 0 168 142 1810
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
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_deg2.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 2.2→2.3 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.4 -8 %
Rwork0.478 924 -
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.478

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