+Open data
-Basic information
Entry | Database: PDB / ID: 3jtt | ||||||
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Title | Cystal structure of Rhesus macaque MHC class I:Mamu-A*02 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / ALPHA HELIX / BETA SHEET / BETA BARREL / Immune response / MHC I / Membrane / Transmembrane / Disease mutation / Disulfide bond / Glycation / Glycoprotein / Immunoglobulin domain / Pyrrolidone carboxylic acid / Secreted | ||||||
Function / homology | Function and homology information antigen processing and presentation of peptide antigen via MHC class I / lumenal side of endoplasmic reticulum membrane / ER to Golgi transport vesicle membrane / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II ...antigen processing and presentation of peptide antigen via MHC class I / lumenal side of endoplasmic reticulum membrane / ER to Golgi transport vesicle membrane / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / recycling endosome membrane / phagocytic vesicle membrane / 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 / early endosome membrane / immune response / lysosomal membrane / virus-mediated perturbation of host defense response / GTP binding / cell surface / extracellular region Similarity search - Function | ||||||
Biological species | Macaca mulatta (Rhesus monkey) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Dai, L. / Feng, Y. / Qi, J. / Gao, G.F. | ||||||
Citation | Journal: To be Published Title: Crystal structure of Rhesus macaque MHC class I:Mamu-A*02 Authors: Dai, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3jtt.cif.gz | 248.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jtt.ent.gz | 201.7 KB | Display | PDB format |
PDBx/mmJSON format | 3jtt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jtt_validation.pdf.gz | 489.9 KB | Display | wwPDB validaton report |
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Full document | 3jtt_full_validation.pdf.gz | 514.9 KB | Display | |
Data in XML | 3jtt_validation.xml.gz | 45.8 KB | Display | |
Data in CIF | 3jtt_validation.cif.gz | 62.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/3jtt ftp://data.pdbj.org/pub/pdb/validation_reports/jt/3jtt | HTTPS FTP |
-Related structure data
Related structure data | 1zvsS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 32106.320 Da / Num. of mol.: 3 / Fragment: UNP residues 17-292 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: Mamu / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q30597 #2: Protein | Mass: 11791.275 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: B2M / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6V7J5 #3: Protein/peptide | Mass: 1014.114 Da / Num. of mol.: 3 / Fragment: UNP residues 159-167 / Source method: obtained synthetically Details: This sequence occurs from Simian immunodeficiency virus References: UniProt: Q9WH73 #4: 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: 3.98 Å3/Da / Density % sol: 69.13 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M Bis-Tris pH 5.5, 2 M ammonium sulfate , VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5478 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 20, 2008 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5478 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 51015 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 57 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 37.2 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 7 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 4.7 / Num. unique all: 4987 / Rsym value: 0.528 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1zvs Resolution: 2.8→31.293 Å / SU ML: 0.4 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.09 / Stereochemistry target values: ML / Details: Used weighted full matrix least squares procedure
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.463 Å2 / ksol: 0.356 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→31.293 Å
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Refine LS restraints |
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LS refinement shell |
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