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- PDB-1p53: The Crystal Structure of ICAM-1 D3-D5 fragment -

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Basic information

Entry
Database: PDB / ID: 1p53
TitleThe Crystal Structure of ICAM-1 D3-D5 fragment
ComponentsIntercellular adhesion molecule-1
KeywordsCELL ADHESION / IgSF domain / beta-sheet / dimer
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 / MIR / Resolution: 3.06 Å
AuthorsYang, Y. / Jun, C.D. / Liu, J.H. / Zhang, R. / Jochimiak, A. / Springer, T.A. / Wang, J.H.
CitationJournal: Mol.Cell / Year: 2004
Title: Structural basis for dimerization of ICAM-1 on the cell surface.
Authors: Yang, Y. / Jun, C.D. / Liu, J.H. / Zhang, R. / Joachimiak, A. / Springer, T.A. / Wang, J.H.
History
DepositionApr 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_asym.entity_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_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-1
B: Intercellular adhesion molecule-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9868
Polymers57,6592
Non-polymers1,3276
Water1,17165
1
A: Intercellular adhesion molecule-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4934
Polymers28,8291
Non-polymers6643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Intercellular adhesion molecule-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4934
Polymers28,8291
Non-polymers6643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)193.700, 193.700, 175.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Intercellular adhesion molecule-1 / / ICAM-1 / Major group rhinovirus receptor / CD54 antigen


Mass: 28829.492 Da / Num. of mol.: 2 / Fragment: ICAM-1 extracellular Domain 3-5, ecto-fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ICAM1 / Plasmid: pBJ5-GS / Cell line (production host): CHO.Lec3.2.8.1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P05362
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
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.: 65 / 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: 5.5 Å3/Da / Density % sol: 77.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 15mg/ml protein, NH4H2PO4, 0.1 M Na-citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.008 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 11, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. all: 23462 / Num. obs: 23462 / % possible obs: 100 % / Observed criterion σ(F): -5 / Observed criterion σ(I): -5 / Redundancy: 7.7 % / Biso Wilson estimate: 65.2 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 10.8
Reflection shellResolution: 3→3.11 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 3.1 / Num. unique all: 2319 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CCP4model building
CNSrefinement
HKL-2000data reduction
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 3.06→20 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2519 2262 10 %RANDOM
Rwork0.2203 ---
all-22760 --
obs-22754 89.9 %-
Displacement parametersBiso mean: 35.184 Å2
Baniso -1Baniso -2Baniso -3
1-2.664 Å2-8.914 Å20 Å2
2--2.664 Å20 Å2
3----5.327 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.39 Å
Luzzati d res low-20 Å
Refinement stepCycle: LAST / Resolution: 3.06→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3806 0 84 65 3955
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007596
X-RAY DIFFRACTIONc_angle_deg1.36572
X-RAY DIFFRACTIONc_dihedral_angle_d28.53881
X-RAY DIFFRACTIONc_improper_angle_d1.27146

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