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- PDB-1sy6: Crystal Structure of CD3gammaepsilon Heterodimer in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 1sy6
TitleCrystal Structure of CD3gammaepsilon Heterodimer in Complex with OKT3 Fab Fragment
Components
  • OKT3 Fab heavy chain
  • OKT3 Fab light chain
  • T-cell surface glycoprotein CD3 gamma/epsilon chain
Keywordssignaling protein/antibiotic / CD3 gamma / CD3 epsilon / OKT3 Fab / signaling protein-antibiotic COMPLEX
Function / homology
Function and homology information


regulation of lymphocyte apoptotic process / gamma-delta T cell receptor complex / T cell anergy / positive regulation of cell-cell adhesion mediated by integrin / positive regulation of T cell anergy / gamma-delta T cell activation / CD4-positive, alpha-beta T cell proliferation / negative thymic T cell selection / positive regulation of CD4-positive, alpha-beta T cell proliferation / alpha-beta T cell receptor complex ...regulation of lymphocyte apoptotic process / gamma-delta T cell receptor complex / T cell anergy / positive regulation of cell-cell adhesion mediated by integrin / positive regulation of T cell anergy / gamma-delta T cell activation / CD4-positive, alpha-beta T cell proliferation / negative thymic T cell selection / positive regulation of CD4-positive, alpha-beta T cell proliferation / alpha-beta T cell receptor complex / positive thymic T cell selection / signal complex assembly / positive regulation of cell-matrix adhesion / T cell receptor complex / smoothened signaling pathway / establishment or maintenance of cell polarity / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of interleukin-4 production / dendrite development / alpha-beta T cell activation / Generation of second messenger molecules / FCGR activation / immunological synapse / Co-inhibition by PD-1 / Role of phospholipids in phagocytosis / T cell receptor binding / T cell costimulation / positive regulation of T cell proliferation / positive regulation of interleukin-2 production / positive regulation of calcium-mediated signaling / FCGR3A-mediated IL10 synthesis / cell surface receptor protein tyrosine kinase signaling pathway / T cell activation / cerebellum development / negative regulation of smoothened signaling pathway / FCGR3A-mediated phagocytosis / apoptotic signaling pathway / calcium-mediated signaling / clathrin-coated endocytic vesicle membrane / Regulation of actin dynamics for phagocytic cup formation / SH3 domain binding / positive regulation of type II interferon production / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Cargo recognition for clathrin-mediated endocytosis / Downstream TCR signaling / transmembrane signaling receptor activity / Clathrin-mediated endocytosis / cell-cell junction / protein transport / T cell receptor signaling pathway / signaling receptor complex adaptor activity / cell body / protein-containing complex assembly / regulation of apoptotic process / dendritic spine / adaptive immune response / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / negative regulation of gene expression / external side of plasma membrane / positive regulation of gene expression / protein kinase binding / endoplasmic reticulum / Golgi apparatus / identical protein binding / plasma membrane / cytosol
Similarity search - Function
CD3 gamma/delta subunit, Ig-like domain / T-cell surface glycoprotein CD3 delta chain / Ig-like domain on T-cell surface glycoprotein CD3 epsilon chain / CD3 protein, epsilon/gamma/delta subunit / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / : / Immunoglobulin subtype 2 ...CD3 gamma/delta subunit, Ig-like domain / T-cell surface glycoprotein CD3 delta chain / Ig-like domain on T-cell surface glycoprotein CD3 epsilon chain / CD3 protein, epsilon/gamma/delta subunit / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
T-cell surface glycoprotein CD3 epsilon chain / T-cell surface glycoprotein CD3 gamma chain / Igh protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKjer-Nielsen, L. / Dunstone, M.A. / Kostenko, L. / Ely, L.K. / Beddoe, T. / Misfud, N.A. / Purcell, A.W. / Brooks, A.G. / McCluskey, J. / Rossjohn, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Crystal structure of the human T cell receptor CD3(epsilon)(gamma) heterodimer complexed to the therapeutic mAb OKT3.
Authors: Kjer-Nielsen, L. / Dunstone, M.A. / Kostenko, L. / Ely, L.K. / Beddoe, T. / Mifsud, N.A. / Purcell, A.W. / Brooks, A.G. / McCluskey, J. / Rossjohn, J.
History
DepositionMar 31, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE The sequence of OKT3 Fab light chain and heavy chain are not available in any of the ...SEQUENCE The sequence of OKT3 Fab light chain and heavy chain are not available in any of the database. The protein T-CELL SURFACE GLYCOPROTEIN CD3 Gamma/epsilon CHAIN has original sequence 0-81 of gamma chain bond to sequence 1-96 of epsilon chain with 26 residues linker (GSADDAKK DAAKKDDAKK DDAKKDGS) in between.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: OKT3 Fab light chain
H: OKT3 Fab heavy chain
A: T-cell surface glycoprotein CD3 gamma/epsilon chain


Theoretical massNumber of molelcules
Total (without water)70,1603
Polymers70,1603
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.702, 55.770, 96.050
Angle α, β, γ (deg.)90.00, 100.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody OKT3 Fab light chain


Mass: 23378.695 Da / Num. of mol.: 1 / Fragment: fab fragment light chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#2: Antibody OKT3 Fab heavy chain


Mass: 23840.611 Da / Num. of mol.: 1 / Fragment: fab fragment heavy chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) / References: UniProt: Q6PJA7*PLUS
#3: Protein T-cell surface glycoprotein CD3 gamma/epsilon chain / T-cell surface antigen T3/Leu-4 gamma/epsilon chain


Mass: 22940.545 Da / Num. of mol.: 1 / Fragment: CD3 epsilon/gamma ecto domain
Source method: isolated from a genetically manipulated source
Details: this protein is composed of gamma and epsilon chains with 26 residues linker
Source: (gene. exp.) Homo sapiens (human) / Gene: CD3G, T3G, CD3E, T3E / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL20 / References: UniProt: P09693, UniProt: P07766
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: 2.54 Å3/Da / Density % sol: 51.52 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG3350, potassium formate, TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 323K, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 16, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 41156
Reflection shellResolution: 2.1→2.17 Å / % possible all: 61.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→50 Å
RfactorNum. reflection
Rfree0.255 -
Rwork0.211 -
all0.211 -
obs0.211 39510
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4651 0 0 0 4651
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.31
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_dihedral_angle_d26.74

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