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Yorodumi- PDB-4yjz: Human antibody H2526 in complex with influenza hemagglutinin H1 S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yjz | ||||||
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Title | Human antibody H2526 in complex with influenza hemagglutinin H1 Solomon Islands/03/2006 | ||||||
Components |
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Keywords | Viral protein/Immune system / influenza / antibody / complex / hemagglutinin / Viral protein-Immune system complex | ||||||
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 | Influenza A virus Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.72 Å | ||||||
Authors | Schmidt, A.G. / Harrison, S.C. | ||||||
Citation | Journal: Cell / Year: 2015 Title: Viral receptor-binding site antibodies with diverse germline origins. Authors: Schmidt, A.G. / Therkelsen, M.D. / Stewart, S. / Kepler, T.B. / Liao, H.X. / Moody, M.A. / Haynes, B.F. / Harrison, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yjz.cif.gz | 105 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yjz.ent.gz | 78.2 KB | Display | PDB format |
PDBx/mmJSON format | 4yjz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yj/4yjz ftp://data.pdbj.org/pub/pdb/validation_reports/yj/4yjz | HTTPS FTP |
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-Related structure data
Related structure data | 4yk4C 3gbnS 4hkxS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 25109.988 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Solomon Islands/3/2006(H1N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A7UPX0 | ||||
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#2: Antibody | Mass: 27967.621 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Mammalia (mammals) | ||||
#3: Sugar | #4: Water | ChemComp-HOH / | Sequence details | Chain L in this structure is a single-chain variable fragment (scFv) which includes the variable ...Chain L in this structure is a single-chain variable fragment (scFv) which includes the variable heavy and variable light domains of an antibody with a linker in-between (GGGGGGSGGG | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.05 Å3/Da / Density % sol: 69.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M HEPES, 30% PEG 400 and 0.1M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99998 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 6, 2014 |
Diffraction measurement | Details: 1.00 degrees, 5.0 sec, detector distance 350.01 mm / Method: \w scans |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99998 Å / Relative weight: 1 |
Reflection | Av R equivalents: 0.07 / Number: 135025 |
Reflection | Resolution: 2.72→50 Å / Num. obs: 23649 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/av σ(I): 39.699 |
Reflection shell | Resolution: 2.72→2.77 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 2.892 / Rsym value: 0.648 / % possible all: 100 |
Cell measurement | Reflection used: 135025 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GBN, 4HKX Resolution: 2.72→39.703 Å / FOM work R set: 0.7241 / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.68 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 182.19 Å2 / Biso mean: 90.78 Å2 / Biso min: 46.68 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.72→39.703 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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