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- PDB-1qa9: Structure of a Heterophilic Adhesion Complex Between the Human CD... -

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Basic information

Entry
Database: PDB / ID: 1qa9
TitleStructure of a Heterophilic Adhesion Complex Between the Human CD2 and CD58(LFA-3) Counter-Receptors
Components
  • HUMAN CD2 PROTEIN
  • HUMAN CD58 PROTEIN
KeywordsIMMUNE SYSTEM / CELL ADHESION / IG-LIKE DOMAIN / CD2 / CD58
Function / homology
Function and homology information


positive regulation of myeloid dendritic cell activation / membrane raft polarization / natural killer cell mediated cytotoxicity / natural killer cell activation / heterotypic cell-cell adhesion / regulation of T cell differentiation / ficolin-1-rich granule membrane / T cell activation / secretory granule membrane / positive regulation of interleukin-8 production ...positive regulation of myeloid dendritic cell activation / membrane raft polarization / natural killer cell mediated cytotoxicity / natural killer cell activation / heterotypic cell-cell adhesion / regulation of T cell differentiation / ficolin-1-rich granule membrane / T cell activation / secretory granule membrane / positive regulation of interleukin-8 production / Cell surface interactions at the vascular wall / cytoplasmic side of plasma membrane / cell-cell adhesion / receptor tyrosine kinase binding / cellular response to type II interferon / : / cell-cell junction / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / signaling receptor activity / cellular response to tumor necrosis factor / cell surface receptor signaling pathway / external side of plasma membrane / signaling receptor binding / apoptotic process / Neutrophil degranulation / Golgi apparatus / cell surface / protein-containing complex / extracellular exosome / extracellular region / nucleoplasm / membrane / identical protein binding / plasma membrane
Similarity search - Function
T-cell surface antigen CD2 / Immunoglobulin C2-set / Immunoglobulin C2-set domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
T-cell surface antigen CD2 / Lymphocyte function-associated antigen 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 3.2 Å
AuthorsWang, J.-H. / Smolyar, A. / Tan, K. / Liu, J.-H. / Kim, M. / Sun, Z.J. / Wagner, G. / Reinherz, E.L.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1999
Title: Structure of a heterophilic adhesion complex between the human CD2 and CD58 (LFA-3) counterreceptors.
Authors: Wang, J.H. / Smolyar, A. / Tan, K. / Liu, J.H. / Kim, M. / Sun, Z.Y. / Wagner, G. / Reinherz, E.L.
#1: Journal: To be Published / Year: 1999
Title: Design and NMR Studies of a Functional Glycan-Free Adhesion Domain of the Human Cell Surface Receptor CD58
Authors: Sun, Z.-Y.J. / Dotsch, V. / Kim, M. / Li, J. / Reinherz, E.L. / Wagner, G.
History
DepositionApr 13, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HUMAN CD2 PROTEIN
B: HUMAN CD58 PROTEIN
C: HUMAN CD2 PROTEIN
D: HUMAN CD58 PROTEIN


Theoretical massNumber of molelcules
Total (without water)46,0424
Polymers46,0424
Non-polymers00
Water0
1
A: HUMAN CD2 PROTEIN
B: HUMAN CD58 PROTEIN


Theoretical massNumber of molelcules
Total (without water)23,0212
Polymers23,0212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: HUMAN CD2 PROTEIN
D: HUMAN CD58 PROTEIN


Theoretical massNumber of molelcules
Total (without water)23,0212
Polymers23,0212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)179.820, 33.470, 108.430
Angle α, β, γ (deg.)90.00, 121.76, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
DetailsThe biological assembly is each of the individual molecules

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Components

#1: Protein HUMAN CD2 PROTEIN


Mass: 12017.655 Da / Num. of mol.: 2 / Fragment: N-TERMINAL ADHESION DOMAIN OF CD2 / Mutation: K61E, F63L, T67A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET-11A / Production host: Escherichia coli (E. coli) / References: UniProt: P06729*PLUS
#2: Protein HUMAN CD58 PROTEIN


Mass: 11003.180 Da / Num. of mol.: 2 / Fragment: N-TERMINAL ADHESION DOMAIN OF CD58 / Mutation: F1S, V9K, V21Q, V58K, T85S, L93G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET-11A / Production host: Escherichia coli (E. coli) / References: UniProt: P19256*PLUS

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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: 3.01 Å3/Da / Density % sol: 59.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 400, (NH4)2SO4, NaCl, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal
*PLUS
Density % sol: 61 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
20.1 MHEPES1drop
32 %PEG4001reservoir
42 Mammonium sulfate1reservoir
51 M1reservoirNaCl
60.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 12, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→18 Å / Num. all: 9453 / Num. obs: 8196 / % possible obs: 86.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 9.8
Reflection shellResolution: 3.2→3.31 Å / Rmerge(I) obs: 0.278 / Num. unique all: 8196 / % possible all: 87.6
Reflection
*PLUS
Num. measured all: 41649
Reflection shell
*PLUS
% possible obs: 87.6 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 3.2→18 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure.
RfactorNum. reflection% reflection
Rfree0.281 778 -
Rwork0.223 --
all-7780 -
obs-7486 96.2 %
Refinement stepCycle: LAST / Resolution: 3.2→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3244 0 0 0 3244
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.102
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.2 Å / σ(F): 2 / Rfactor obs: 0.223
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_bond_d / Dev ideal: 0.006

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