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Yorodumi- PDB-4nkj: Structure of influenza B virus hemagglutinin at membrane fusion pH -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nkj | ||||||
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Title | Structure of influenza B virus hemagglutinin at membrane fusion pH | ||||||
Components | Hemagglutinin HA2 | ||||||
Keywords | VIRAL PROTEIN / HA | ||||||
Function / homology | Function and homology information viral budding from plasma membrane / endocytosis involved in viral entry into 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 B virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4535 Å | ||||||
Authors | Ni, F. / Chen, X. / Shen, J. / Wang, Q. | ||||||
Citation | Journal: Biochemistry / Year: 2014 Title: Structural insights into the membrane fusion mechanism mediated by influenza virus hemagglutinin. Authors: Ni, F. / Chen, X. / Shen, J. / Wang, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nkj.cif.gz | 35 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nkj.ent.gz | 27.3 KB | Display | PDB format |
PDBx/mmJSON format | 4nkj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nkj_validation.pdf.gz | 428.4 KB | Display | wwPDB validaton report |
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Full document | 4nkj_full_validation.pdf.gz | 435.4 KB | Display | |
Data in XML | 4nkj_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 4nkj_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nk/4nkj ftp://data.pdbj.org/pub/pdb/validation_reports/nk/4nkj | 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 17211.225 Da / Num. of mol.: 1 / Fragment: Hemagglutinin HA2 (UNP Residues 392-541) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza B virus / Gene: HA / Production host: Escherichia coli (E. coli) / References: UniProt: S5DRP1 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.59 % |
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-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.127 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.127 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→37.76 Å / Num. all: 6281 / Num. obs: 5617 / % possible obs: 89.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.45→2.54 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 5.21 / Num. unique all: 615 / % possible all: 94.96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4535→37.758 Å / SU ML: 0.27 / σ(F): 1.94 / Phase error: 32.86 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.41 Å2 / ksol: 0.358 e/Å3 | ||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.4535→37.758 Å
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Refine LS restraints |
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LS refinement shell |
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