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Yorodumi- PDB-6oc3: Crystal structure of FluA-20 Fab in complex with the head domain ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6oc3 | ||||||
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Title | Crystal structure of FluA-20 Fab in complex with the head domain of H1 (A/Solomon Islands/3/2006) | ||||||
Components |
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Keywords | IMMUNE SYSTEM / anti-flu antibody / HA head domain | ||||||
Function / homology | Function and homology information viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Wilson, I.A. / Lang, S. | ||||||
Citation | Journal: Cell / Year: 2019 Title: A Site of Vulnerability on the Influenza Virus Hemagglutinin Head Domain Trimer Interface. Authors: Bangaru, S. / Lang, S. / Schotsaert, M. / Vanderven, H.A. / Zhu, X. / Kose, N. / Bombardi, R. / Finn, J.A. / Kent, S.J. / Gilchuk, P. / Gilchuk, I. / Turner, H.L. / Garcia-Sastre, A. / Li, S. ...Authors: Bangaru, S. / Lang, S. / Schotsaert, M. / Vanderven, H.A. / Zhu, X. / Kose, N. / Bombardi, R. / Finn, J.A. / Kent, S.J. / Gilchuk, P. / Gilchuk, I. / Turner, H.L. / Garcia-Sastre, A. / Li, S. / Ward, A.B. / Wilson, I.A. / 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 | 6oc3.cif.gz | 261.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6oc3.ent.gz | 207.9 KB | Display | PDB format |
PDBx/mmJSON format | 6oc3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/6oc3 ftp://data.pdbj.org/pub/pdb/validation_reports/oc/6oc3 | HTTPS FTP |
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-Related structure data
Related structure data | 6obzSC 6ocbC 4yjzS 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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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 25154.039 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #2: Antibody | Mass: 23508.186 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #3: Protein | Mass: 25700.635 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/Solomon Islands/3/2006(H1N1)) Strain: A/Solomon Islands/3/2006(H1N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A7Y8I1 #4: Sugar | ChemComp-NAG / | |
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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: 2.78 Å3/Da / Density % sol: 55.73 % |
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Crystal grow | Temperature: 277.12 K / Method: vapor diffusion, sitting drop / Details: 0.1 M phosphate-citrate, pH 4.2 40%(v/v) PEG300 |
-Data collection
Diffraction | Mean temperature: 78 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03315 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03315 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→50 Å / Num. obs: 36821 / % possible obs: 95.7 % / Redundancy: 6.8 % / CC1/2: 1 / Rpim(I) all: 0.05 / Rsym value: 0.13 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 2.85→2.9 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1436 / CC1/2: 0.91 / Rpim(I) all: 0.31 / Rsym value: 0.78 / % possible all: 74.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YJZ and 6OBZ Resolution: 2.85→48.168 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.41 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→48.168 Å
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Refine LS restraints |
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LS refinement shell |
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