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Yorodumi- PDB-6vy6: Crystal structure of Hendra receptor binding protein head domain ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vy6 | ||||||
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Title | Crystal structure of Hendra receptor binding protein head domain in complex with human neutralizing antibody HENV-26 | ||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / henipavirus / Hendra virus / receptor binding protein / antibody / antibody-antigen complex / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information exo-alpha-sialidase activity / host cell surface / host cell surface receptor binding / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Hendra henipavirus Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å | ||||||
Authors | Dong, J. / Crowe, J.E. | ||||||
Funding support | United States, 1items
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Citation | Journal: Cell / Year: 2020 Title: Potent Henipavirus Neutralization by Antibodies Recognizing Diverse Sites on Hendra and Nipah Virus Receptor Binding Protein. Authors: Dong, J. / Cross, R.W. / Doyle, M.P. / Kose, N. / Mousa, J.J. / Annand, E.J. / Borisevich, V. / Agans, K.N. / Sutton, R. / Nargi, R. / Majedi, M. / Fenton, K.A. / Reichard, W. / Bombardi, R. ...Authors: Dong, J. / Cross, R.W. / Doyle, M.P. / Kose, N. / Mousa, J.J. / Annand, E.J. / Borisevich, V. / Agans, K.N. / Sutton, R. / Nargi, R. / Majedi, M. / Fenton, K.A. / Reichard, W. / Bombardi, R.G. / Geisbert, T.W. / Crowe Jr., J.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vy6.cif.gz | 353.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vy6.ent.gz | 283.8 KB | Display | PDB format |
PDBx/mmJSON format | 6vy6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/6vy6 ftp://data.pdbj.org/pub/pdb/validation_reports/vy/6vy6 | HTTPS FTP |
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-Related structure data
Related structure data | 6vy4C 6vy5C 2x9mS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Anti-Hendra receptor binding protein antibody HENV-26 Fab ... , 2 types, 2 molecules HL
#2: Protein | Mass: 24446.480 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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#3: Protein | Mass: 22755.068 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
-Protein / Sugars , 2 types, 5 molecules A
#1: Protein | Mass: 48887.309 Da / Num. of mol.: 1 / Fragment: head domain (UNP residues 185-604) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hendra henipavirus / Production host: Homo sapiens (human) / References: UniProt: F4YH71, UniProt: O89343*PLUS |
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#6: Sugar | ChemComp-NAG / |
-Non-polymers , 5 types, 199 molecules
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-MPD / ( | #7: Chemical | ChemComp-CL / | #8: Chemical | ChemComp-ZN / | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.6 Å3/Da / Density % sol: 52.75 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 30% MPD, 0.1 imidazole, pH 6.5, 0.2 M ammonium sulfate, 10% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jun 26, 2018 |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→47.46 Å / Num. obs: 31674 / % possible obs: 99.9 % / Redundancy: 14.8 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.6→2.74 Å / Rmerge(I) obs: 0.757 / Num. unique obs: 4550 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2X9M Resolution: 2.6→45.347 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.78
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 172.07 Å2 / Biso mean: 52.0148 Å2 / Biso min: 26.39 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→45.347 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: -11.9176 Å / Origin y: 95.7803 Å / Origin z: 40.4917 Å
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Refinement TLS group |
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