+Open data
-Basic information
Entry | Database: PDB / ID: 8hsm | ||||||
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Title | CRYSTAL STRUCTURE OF BAT MHC CLASS I MYLU-B-67 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / MHC / IMMUNOLIGY / IMMUNE SYSTEM TRANSFERASE COMPLEX. | ||||||
Function / homology | Function and homology information antigen processing and presentation of peptide antigen via MHC class I / lumenal side of endoplasmic reticulum membrane / MHC class I protein complex / phagocytic vesicle membrane / immune response / extracellular region Similarity search - Function | ||||||
Biological species | Myotis lucifugus (little brown bat) Pteropus alecto (black flying fox) Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Wang, S.Q. / Zhang, N.Z. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: CRYSTAL STRUCTURE OF BAT MHC CLASS I MYLU-B-67 Authors: Wang, S.Q. / Zhang, N.Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hsm.cif.gz | 94.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hsm.ent.gz | 70.3 KB | Display | PDB format |
PDBx/mmJSON format | 8hsm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hs/8hsm ftp://data.pdbj.org/pub/pdb/validation_reports/hs/8hsm | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 32112.572 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Myotis lucifugus (little brown bat) / Gene: B-67 / Production host: Escherichia coli (E. coli) / References: UniProt: G1PNR4 |
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#2: Protein | Mass: 11474.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pteropus alecto (black flying fox) / Gene: PAL_GLEAN10023531 / Production host: Escherichia coli (E. coli) / References: UniProt: L5K3Y9 |
#3: Protein/peptide | Mass: 940.032 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Production host: Escherichia coli (E. coli) |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.18 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7.3 Details: 0.2M Sodium fluoride,20%w/v Polyethylene glycol 3350, |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 5, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→50 Å / Num. obs: 23370 / % possible obs: 99.9 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 24.714 |
Reflection shell | Resolution: 2.18→2.22 Å / Rmerge(I) obs: 1.17 / Num. unique obs: 1150 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.911 / SU B: 7.358 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.358 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.79 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→30 Å
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Refine LS restraints |
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