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Yorodumi- PDB-1sy6: Crystal Structure of CD3gammaepsilon Heterodimer in Complex with ... -
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-Basic information
Entry | Database: PDB / ID: 1sy6 | ||||||
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Title | Crystal Structure of CD3gammaepsilon Heterodimer in Complex with OKT3 Fab Fragment | ||||||
Components |
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Keywords | signaling 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 T cell anergy / positive regulation of cell-cell adhesion mediated by integrin / CD4-positive, alpha-beta T cell proliferation / gamma-delta T cell activation / 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 T cell anergy / positive regulation of cell-cell adhesion mediated by integrin / CD4-positive, alpha-beta T cell proliferation / gamma-delta T cell activation / 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 / positive regulation of interleukin-4 production / dendrite development / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / immunological synapse / FCGR activation / PD-1 signaling / Role of phospholipids in phagocytosis / positive regulation of calcium-mediated signaling / T cell receptor binding / negative regulation of smoothened signaling pathway / positive regulation of T cell proliferation / cell surface receptor protein tyrosine kinase signaling pathway / T cell costimulation / positive regulation of interleukin-2 production / T cell activation / cerebellum development / FCGR3A-mediated IL10 synthesis / calcium-mediated signaling / apoptotic signaling pathway / FCGR3A-mediated phagocytosis / clathrin-coated endocytic vesicle membrane / Regulation of actin dynamics for phagocytic cup formation / SH3 domain binding / transmembrane signaling receptor activity / positive regulation of peptidyl-tyrosine phosphorylation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of type II interferon production / cell-cell junction / signaling receptor complex adaptor activity / protein transport / Cargo recognition for clathrin-mediated endocytosis / Downstream TCR signaling / Clathrin-mediated endocytosis / T cell receptor signaling pathway / cell body / protein-containing complex assembly / regulation of apoptotic process / adaptive immune response / dendritic spine / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / external side of plasma membrane / negative regulation of gene expression / positive regulation of gene expression / protein kinase binding / Golgi apparatus / endoplasmic reticulum / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Kjer-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. | ||||||
Citation | Journal: 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 |
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Remark 999 | SEQUENCE 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sy6.cif.gz | 122.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sy6.ent.gz | 98.8 KB | Display | PDB format |
PDBx/mmJSON format | 1sy6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sy6_validation.pdf.gz | 380 KB | Display | wwPDB validaton report |
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Full document | 1sy6_full_validation.pdf.gz | 389.4 KB | Display | |
Data in XML | 1sy6_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 1sy6_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sy/1sy6 ftp://data.pdbj.org/pub/pdb/validation_reports/sy/1sy6 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | 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) |
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#2: Antibody | 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 | 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 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.52 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 16, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 41156 |
Reflection shell | Resolution: 2.1→2.17 Å / % possible all: 61.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→50 Å
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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