[English] 日本語
Yorodumi- PDB-4o5n: Crystal structure of A/Victoria/361/2011 (H3N2) influenza virus h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4o5n | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of A/Victoria/361/2011 (H3N2) influenza virus hemagglutinin | |||||||||
Components | (Hemagglutinin ...) x 2 | |||||||||
Keywords | VIRAL PROTEIN / viral fusion protein / virus attachment and entry | |||||||||
Function / homology | Function and homology information viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | |||||||||
Authors | Lee, P.S. / Wilson, I.A. | |||||||||
Citation | Journal: Nat Commun / Year: 2014 Title: Receptor mimicry by antibody F045-092 facilitates universal binding to the H3 subtype of influenza virus. Authors: Lee, P.S. / Ohshima, N. / Stanfield, R.L. / Yu, W. / Iba, Y. / Okuno, Y. / Kurosawa, Y. / Wilson, I.A. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4o5n.cif.gz | 227.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4o5n.ent.gz | 182.4 KB | Display | PDB format |
PDBx/mmJSON format | 4o5n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4o5n_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4o5n_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4o5n_validation.xml.gz | 25.1 KB | Display | |
Data in CIF | 4o5n_validation.cif.gz | 37.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o5/4o5n ftp://data.pdbj.org/pub/pdb/validation_reports/o5/4o5n | HTTPS FTP |
-Related structure data
Related structure data | 4o58C 4o5iC 4o5lC 2yp7S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Hemagglutinin ... , 2 types, 2 molecules AB
#1: Protein | Mass: 35934.473 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Singapore/H2011.447/2011(H3N2) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: R9U684, UniProt: A0A097PF39*PLUS |
---|---|
#2: Protein | Mass: 20153.393 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Singapore/H2011.447/2011(H3N2) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: R9U684, UniProt: L0HR89*PLUS |
-Sugars , 3 types, 6 molecules
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
---|---|
#4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 435 molecules
#6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-PEG / | #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.1 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.7 Details: 5% PEG 8,000, 20% PEG 300, 10% glycerol, 0.1 M Tris pH 8.7, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 77 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2013 |
Radiation | Monochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. all: 75930 / Num. obs: 75930 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 1.75→1.85 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.89 / % possible all: 99 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YP7 Resolution: 1.75→46.839 Å / SU ML: 0.15 / σ(F): 2 / Phase error: 18.01 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→46.839 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|