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- PDB-1t0p: Structural Basis of ICAM recognition by integrin alpahLbeta2 reve... -

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Basic information

Entry
Database: PDB / ID: 1t0p
TitleStructural Basis of ICAM recognition by integrin alpahLbeta2 revealed in the complex structure of binding domains of ICAM-3 and alphaLbeta2 at 1.65 A
Components
  • Integrin alpha-L
  • Intercellular adhesion molecule-3
KeywordsIMMUNE SYSTEM / Rossmann Fold / IG-super family domain
Function / homology
Function and homology information


memory T cell extravasation / integrin alphaL-beta2 complex / ICAM-3 receptor activity / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / RUNX3 Regulates Immune Response and Cell Migration / integrin complex / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / cell adhesion mediated by integrin / leukocyte cell-cell adhesion / receptor clustering ...memory T cell extravasation / integrin alphaL-beta2 complex / ICAM-3 receptor activity / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / RUNX3 Regulates Immune Response and Cell Migration / integrin complex / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / cell adhesion mediated by integrin / leukocyte cell-cell adhesion / receptor clustering / Integrin cell surface interactions / specific granule membrane / phagocytosis / cell adhesion molecule binding / CD209 (DC-SIGN) signaling / cell-matrix adhesion / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / cell-cell adhesion / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / cell adhesion / inflammatory response / external side of plasma membrane / signaling receptor binding / Neutrophil degranulation / cell surface / signal transduction / extracellular exosome / membrane / metal ion binding / 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 / : / Integrin alpha cytoplasmic region / von Willebrand factor, type A domain / Integrin alpha-2 ...: / 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 / : / Integrin alpha cytoplasmic region / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Integrin alpha-L / Intercellular adhesion molecule 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsSong, G. / Yang, Y.T. / Liu, J.H. / Shimaoko, M. / Springer, T.A. / Wang, J.H.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: An atomic resolution view of ICAM recognition in a complex between the binding domains of ICAM-3 and integrin alphaLbeta2.
Authors: Song, G. / Yang, Y. / Liu, J.H. / Casasnovas, J.M. / Shimaoka, M. / Springer, T.A. / Wang, J.H.
History
DepositionApr 12, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 27, 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 1.5Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrin alpha-L
B: Intercellular adhesion molecule-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4045
Polymers28,9372
Non-polymers4673
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-5 kcal/mol
Surface area12540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.463, 66.471, 110.816
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein Integrin alpha-L / cell surface glycoprotein CD11a / antigen CD11A (p180) / lymphocyte function-associated antigen 1 / CD11a


Mass: 19911.711 Da / Num. of mol.: 1 / Fragment: I domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P20701
#2: Protein Intercellular adhesion molecule-3 / ICAM-3 / ICAM-R / CDw50 / CD50 antigen


Mass: 9025.093 Da / Num. of mol.: 1 / Fragment: domain 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): Lec Cells / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P32942
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: PEG MME 5000, (NH4)2SO4, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 160 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Aug 3, 2003
RadiationMonochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.66→50 Å / Num. all: 35921 / Num. obs: 35921 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.66→1.71 Å / % possible all: 92.3

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2413 3578 Random
Rwork0.2204 --
all-35869 -
obs-35869 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.899 Å20 Å20 Å2
2---1.315 Å20 Å2
3---5.215 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.66→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2021 0 29 169 2219
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00503
X-RAY DIFFRACTIONc_angle_deg1.24336
X-RAY DIFFRACTIONc_dihedral_angle_d25.20975
X-RAY DIFFRACTIONc_improper_angle_d1.08028

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