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- PDB-1zon: CD11A I-DOMAIN WITHOUT BOUND CATION -

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Basic information

Entry
Database: PDB / ID: 1zon
TitleCD11A I-DOMAIN WITHOUT BOUND CATION
ComponentsLEUKOCYTE ADHESION GLYCOPROTEIN
KeywordsCELL ADHESION / INTEGRIN / GLYCOPROTEIN / TRANSMEMBRANE / EXTRACELLULAR MATRIX / CYTOSKELETON
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 / heterophilic cell-cell adhesion / integrin complex / leukocyte cell-cell adhesion / cell adhesion mediated by integrin / 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 / heterophilic cell-cell adhesion / integrin complex / leukocyte cell-cell adhesion / cell adhesion mediated by integrin / receptor clustering / phagocytosis / Integrin cell surface interactions / specific granule membrane / cell adhesion molecule binding / cell-matrix adhesion / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / cell-cell adhesion / integrin binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell adhesion / inflammatory response / external side of plasma membrane / Neutrophil degranulation / cell surface / signal transduction / extracellular exosome / metal ion binding / membrane / plasma membrane
Similarity search - Function
Integrin alpha cytoplasmic region / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / Integrin alpha chain / Integrin alpha beta-propellor / : / Integrin alpha Ig-like domain 2 ...Integrin alpha cytoplasmic region / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / Integrin alpha chain / Integrin alpha beta-propellor / : / Integrin alpha Ig-like domain 2 / 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 / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsLeahy, D.J. / Qu, A.
Citation
Journal: Structure / Year: 1996
Title: The role of the divalent cation in the structure of the I domain from the CD11a/CD18 integrin.
Authors: Qu, A. / Leahy, D.J.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: Crystal Structure of the I-Domain from the Cd11A/Cd18 (Lfa-1, Alpha L Beta 2) Integrin
Authors: Qu, A. / Leahy, D.J.
History
DepositionJun 20, 1996Processing site: BNL
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LEUKOCYTE ADHESION GLYCOPROTEIN


Theoretical massNumber of molelcules
Total (without water)21,3231
Polymers21,3231
Non-polymers00
Water1,820101
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.090, 63.690, 40.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein LEUKOCYTE ADHESION GLYCOPROTEIN / LFA-1 / CD11A/CD18 / ALPHAL BETA2 INTEGRIN / A-DOMAIN


Mass: 21323.494 Da / Num. of mol.: 1 / Fragment: I-DOMAIN FRAGMENT OF LFA-1 / Mutation: W189R, MIGHT BE ISOFORM
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCR PRODUCT / Plasmid: PET11C / Gene (production host): PCR PRODUCT / Production host: Escherichia coli (E. coli) / References: UniProt: P20701
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 1.89 Å3/Da / Density % sol: 35.02 %
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-20 mg/mlCD11a I domain1drop
22 mMEDTA1drop
35 mMbeta-mercaptoethanol1drop
430-33 %PEG33501reservoir
51 mMEDTA1reservoir
630 mMTris-HCl1reservoir
72 mMbeta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9686, 0.9791, 0.9793, 0.9879
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Feb 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.96861
20.97911
30.97931
40.98791
ReflectionNum. obs: 11039 / % possible obs: 96.4 % / Redundancy: 10 % / Rmerge(I) obs: 0.11
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 30 Å

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementResolution: 2→6 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.243 -5 %
Rwork0.184 --
obs0.184 10129 88.4 %
Displacement parametersBiso mean: 21.92 Å2
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1458 0 0 110 1568
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_deg1.9
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_d1.24
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it0.98
X-RAY DIFFRACTIONx_mcangle_it1.1
X-RAY DIFFRACTIONx_scbond_it1.74
X-RAY DIFFRACTIONx_scangle_it1.82
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS

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