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Yorodumi- PDB-4wa2: The crystal structure of hemagglutinin from a H3N8 influenza viru... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wa2 | |||||||||
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Title | The crystal structure of hemagglutinin from a H3N8 influenza virus isolated from New England harbor seals in complex with 3'SLN | |||||||||
Components | Hemagglutinin | |||||||||
Keywords | VIRAL PROTEIN / hemagglutinin / influenza virus / seal | |||||||||
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 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å | |||||||||
Authors | Yang, H. / Villanueva, J.M. / Gubareva, L.V. / Stevens, J. | |||||||||
Citation | Journal: J.Virol. / Year: 2015 Title: Structural and Functional Analysis of Surface Proteins from an A(H3N8) Influenza Virus Isolated from New England Harbor Seals. Authors: Yang, H. / Nguyen, H.T. / Carney, P.J. / Guo, Z. / Chang, J.C. / Jones, J. / Davis, C.T. / Villanueva, J.M. / Gubareva, L.V. / Stevens, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wa2.cif.gz | 607 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wa2.ent.gz | 499.1 KB | Display | PDB format |
PDBx/mmJSON format | 4wa2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wa2_validation.pdf.gz | 4.3 MB | Display | wwPDB validaton report |
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Full document | 4wa2_full_validation.pdf.gz | 4.4 MB | Display | |
Data in XML | 4wa2_validation.xml.gz | 114.1 KB | Display | |
Data in CIF | 4wa2_validation.cif.gz | 160 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/4wa2 ftp://data.pdbj.org/pub/pdb/validation_reports/wa/4wa2 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 8 - 503 / Label seq-ID: 1 - 496
NCS ensembles :
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-Components
-Protein / Non-polymers , 2 types, 1059 molecules ABCDEF
#1: Protein | Mass: 55662.246 Da / Num. of mol.: 6 / Fragment: UNP residues 24-519 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/harbor seal/Massachusetts/1/2011(H3N8)) Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: I6NNE1 #6: Water | ChemComp-HOH / | |
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-Sugars , 4 types, 22 molecules
#2: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #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 | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.51 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / Details: 0.2 M ammonium iodide, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 11, 2013 |
Radiation | Monochromator: Side scattering I-beam bent single crystal, asymmetric cut 4.9650 degrees Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 119563 / Num. obs: 115418 / % possible obs: 96.5 % / Redundancy: 3.7 % / Net I/σ(I): 15.4 |
-Processing
Software | Name: REFMAC / Version: 5.7.0029 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.5→45.19 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.92 / SU B: 17.636 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.733 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.461 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→45.19 Å
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Refine LS restraints |
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