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Yorodumi- PDB-1xiw: Crystal structure of human CD3-e/d dimer in complex with a UCHT1 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xiw | ||||||
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Title | Crystal structure of human CD3-e/d dimer in complex with a UCHT1 single-chain antibody fragment | ||||||
Components |
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Keywords | membrane protein/Immune System / CD3-epsilon / CD3-delta / UCHT1-scFv / immunoglobulin fold / antibody-antigen complex / membrane protein-Immune System COMPLEX | ||||||
Function / homology | Function and homology information 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 ...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 / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / dendrite development / Generation of second messenger molecules / alpha-beta T cell activation / immunological synapse / PD-1 signaling / positive regulation of interleukin-4 production / negative regulation of smoothened signaling pathway / positive regulation of calcium-mediated signaling / positive regulation of T cell proliferation / T cell costimulation / positive regulation of interleukin-2 production / T cell receptor binding / cerebellum development / T cell activation / calcium-mediated signaling / apoptotic signaling pathway / clathrin-coated endocytic vesicle membrane / SH3 domain binding / cell surface receptor protein tyrosine kinase signaling pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of peptidyl-tyrosine phosphorylation / cell-cell junction / transmembrane signaling receptor activity / positive regulation of type II interferon production / signaling receptor complex adaptor activity / Cargo recognition for clathrin-mediated endocytosis / Downstream TCR signaling / Clathrin-mediated endocytosis / cell body / T cell receptor signaling pathway / protein-containing complex assembly / regulation of apoptotic process / dendritic spine / adaptive immune response / 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 / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Arnett, K.L. / Harrison, S.C. / Wiley, D.C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2004 Title: Crystal structure of a human CD3-epsilon/delta dimer in complex with a UCHT1 single-chain antibody fragment. Authors: Arnett, K.L. / Harrison, S.C. / Wiley, D.C. | ||||||
History |
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Remark 999 | SEQUENCE The chimera protein consists of immunoglobulin light chain variable region (chains C, G), ...SEQUENCE The chimera protein consists of immunoglobulin light chain variable region (chains C, G), a linker GGGGSGGGGSGGGGS, and immunoglobulin heavy chain variable region (chains D, H). However, the linker GGGGSGGGGSGGGGS are not modeled due to disorder. The conflicts are due to immunoglobulin domain variable region (v) |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xiw.cif.gz | 167.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xiw.ent.gz | 132.9 KB | Display | PDB format |
PDBx/mmJSON format | 1xiw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xi/1xiw ftp://data.pdbj.org/pub/pdb/validation_reports/xi/1xiw | HTTPS FTP |
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-Related structure data
Related structure data | 6fabS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 11893.056 Da / Num. of mol.: 2 / Fragment: ectodomain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD3E, T3E / Plasmid: pLM1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07766 #2: Protein | Mass: 9106.425 Da / Num. of mol.: 2 / Fragment: ectodomain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD3D, T3D / Plasmid: pLM1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04234 #3: Antibody | Mass: 11994.338 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: UCHT1 / Plasmid: pET17b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: PIR: PH0888 #4: Antibody | Mass: 13650.221 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: UCHT1 / Plasmid: pET17b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: PIR: PH0887 #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 39.8 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 3350, sodium chloride, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 22K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9796 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 6, 2003 |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 62308 / Num. obs: 60988 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 24.4 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 4.7 / Num. unique all: 6134 / Rsym value: 0.357 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 6FAB Resolution: 1.9→49.17 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2409958.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.2681 Å2 / ksol: 0.361556 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→49.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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