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Yorodumi- PDB-4zso: Crystal structure of a complex between B7-H6, a tumor cell ligand... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zso | |||||||||
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Title | Crystal structure of a complex between B7-H6, a tumor cell ligand for natural cytotoxicity receptor NKp30, and an inhibitory antibody | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / Tumor ligand B7-H6 / Antibody | |||||||||
Function / homology | Function and homology information MHC class I protein complex binding / TAP complex binding / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / peptide antigen assembly with MHC class I protein complex / MHC class I peptide loading complex / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antibacterial humoral response / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Xu, X. / Li, Y. / Mariuzza, R.A. | |||||||||
Citation | Journal: to be published Title: Crystal structure of a complex between B7-H6, a tumor cell ligand for natural cytotoxicity receptor NKp30, and an inhibitory antibody Authors: Xu, X. / Li, Y. / Vivier, E. / Chen, Q. / Mariuzza, R.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zso.cif.gz | 260.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zso.ent.gz | 211.8 KB | Display | PDB format |
PDBx/mmJSON format | 4zso.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zso_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 4zso_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 4zso_validation.xml.gz | 50.4 KB | Display | |
Data in CIF | 4zso_validation.cif.gz | 70 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/4zso ftp://data.pdbj.org/pub/pdb/validation_reports/zs/4zso | HTTPS FTP |
-Related structure data
Similar structure data |
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-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
-Protein , 1 types, 2 molecules EF
#3: Protein | Mass: 28319.947 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NCR3LG1, B7H6 / Production host: unidentified baculovirus / References: UniProt: Q68D85 |
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-Antibody , 2 types, 4 molecules ACBD
#1: Antibody | Mass: 23508.086 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-26b / Production host: Escherichia Coli (E. coli) / Strain (production host): BL21(DE3) #2: Antibody | Mass: 23249.070 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) |
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-Sugars , 3 types, 4 molecules
#4: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
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#5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source |
-Non-polymers , 3 types, 255 molecules
#7: Chemical | #8: Chemical | #9: 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: 3.53 Å3/Da / Density % sol: 65.17 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 8 Details: PEG 8000, Tris-HCl, lithium sulfate, calcium acetate PH range: 7.0-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.502 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 20, 2014 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.502 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 74515 / % possible obs: 100 % / Redundancy: 14.4 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.783 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→50 Å / Cross valid method: FREE R-VALUE / σ(F): 0
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Solvent computation | Bsol: 32.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.45 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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Xplor file |
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