+Open data
-Basic information
Entry | Database: PDB / ID: 1zgl | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of 3A6 TCR bound to MBP/HLA-DR2a | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / TCR-peptide-MHC complex | ||||||
Function / homology | Function and homology information compact myelin / structural constituent of myelin sheath / positive regulation of metalloendopeptidase activity / : / internode region of axon / axon ensheathment / negative regulation of heterotypic cell-cell adhesion / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane ...compact myelin / structural constituent of myelin sheath / positive regulation of metalloendopeptidase activity / : / internode region of axon / axon ensheathment / negative regulation of heterotypic cell-cell adhesion / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / EGR2 and SOX10-mediated initiation of Schwann cell myelination / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / membrane organization / alpha-beta T cell receptor complex / positive regulation of memory T cell differentiation / positive regulation of chemokine (C-X-C motif) ligand 2 production / transport vesicle membrane / polysaccharide binding / maintenance of blood-brain barrier / 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 / PD-1 signaling / T cell receptor binding / substantia nigra development / MHC class II antigen presentation / myelination / trans-Golgi network membrane / clathrin-coated endocytic vesicle membrane / central nervous system development / cell periphery / lumenal side of endoplasmic reticulum membrane / sensory perception of sound / response to bacterium / ER to Golgi transport vesicle membrane / response to toxic substance / cognition / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / positive regulation of interleukin-6 production / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / endocytic vesicle membrane / Interferon gamma signaling / positive regulation of immune response / MAPK cascade / positive regulation of T cell activation / Downstream TCR signaling / myelin sheath / MHC class II protein complex binding / early endosome membrane / late endosome membrane / T cell receptor signaling pathway / protease binding / chemical synaptic transmission / adaptive immune response / calmodulin binding / lysosome / immune response / Golgi membrane / lysosomal membrane / neuronal cell body / lipid binding / synapse / cell surface / protein-containing complex / extracellular exosome / membrane / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Li, Y. / Huang, Y. / Lue, J. / Quandt, J.A. / Martin, R. / Mariuzza, R.A. | ||||||
Citation | Journal: Embo J. / Year: 2005 Title: Structure of a human autoimmune TCR bound to a myelin basic protein self-peptide and a multiple sclerosis-associated MHC class II molecule. Authors: Li, Y. / Huang, Y. / Lue, J. / Quandt, J.A. / Martin, R. / Mariuzza, R.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1zgl.cif.gz | 602 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1zgl.ent.gz | 485.8 KB | Display | PDB format |
PDBx/mmJSON format | 1zgl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zgl_validation.pdf.gz | 594.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1zgl_full_validation.pdf.gz | 824.8 KB | Display | |
Data in XML | 1zgl_validation.xml.gz | 134.3 KB | Display | |
Data in CIF | 1zgl_validation.cif.gz | 179.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zg/1zgl ftp://data.pdbj.org/pub/pdb/validation_reports/zg/1zgl | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 21084.826 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA / Plasmid: pET-26b / Production host: Escherichia coli (E. coli) / References: UniProt: P01903 #2: Protein | Mass: 22446.783 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-26b / Production host: Escherichia coli (E. coli) / References: UniProt: Q29787, UniProt: Q30154*PLUS #3: Protein/peptide | Mass: 1672.946 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens / References: UniProt: Q6AI64, UniProt: P02686*PLUS #4: Protein | Mass: 22932.279 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-26b / Production host: Escherichia coli (E. coli) / References: UniProt: P01848 #5: Protein | Mass: 27794.729 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-26b / Production host: Escherichia coli (E. coli) / References: UniProt: P01850 |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.29 % |
---|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Oct 1, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. all: 177348 / Num. obs: 81551 / % possible obs: 0.863 % / Observed criterion σ(F): 5.9 / Observed criterion σ(I): 5.9 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 |
Reflection shell | Resolution: 2.8→2.92 Å / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.284 / % possible all: 86.5 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→30 Å
|