+Open data
-Basic information
Entry | Database: PDB / ID: 2z31 | ||||||
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Title | Crystal structure of immune receptor complex | ||||||
Components |
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Keywords | IMMUNE SYSTEM / complex | ||||||
Function / homology | Function and homology information antigen processing and presentation of peptide antigen / positive regulation of T cell differentiation / antigen processing and presentation / negative regulation of T cell proliferation / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation ...antigen processing and presentation of peptide antigen / positive regulation of T cell differentiation / antigen processing and presentation / negative regulation of T cell proliferation / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / adaptive immune response / lysosome / lysosomal membrane / external side of plasma membrane / protein-containing complex binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Feng, D. / Bond, C.J. / Ely, L.K. / Garcia, K.C. | ||||||
Citation | Journal: Nat.Immunol. / Year: 2007 Title: Structural evidence for a germline-encoded T cell receptor-major histocompatibility complex interaction 'codon' Authors: Feng, D. / Bond, C.J. / Ely, L.K. / Maynard, J. / Garcia, K.C. | ||||||
History |
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Remark 999 | SEQUENCE The sequnce database for chain A and B does not currently exist in UNP. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z31.cif.gz | 126 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z31.ent.gz | 102.8 KB | Display | PDB format |
PDBx/mmJSON format | 2z31.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z3/2z31 ftp://data.pdbj.org/pub/pdb/validation_reports/z3/2z31 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12379.511 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5R1F5 |
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#2: Protein | Mass: 12010.091 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: A2NTY6 |
#3: Protein | Mass: 20540.934 Da / Num. of mol.: 1 / Fragment: extracellular alpha-1 and extracellular alpha-2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P14438 |
#4: Protein | Mass: 22495.164 Da / Num. of mol.: 1 / Fragment: extracellular beta-1 and extracellular beta-2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P06344 |
#5: Protein/peptide | Mass: 1208.286 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.1 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2M patassium sodium tartrate tetrahydrate, 0.1M succinic acid, 16% polyethylene glycol 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.7→97 Å / Num. all: 23722 / Num. obs: 23722 / % possible obs: 99.8 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 2.7→2.78 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 2.7 / Num. unique all: 23722 / Rsym value: 0.549 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→50 Å
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Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
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