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Yorodumi- PDB-4d00: Haemagglutinin of H10N8 Influenza Virus Isolated from Humans in C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4d00 | |||||||||
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Title | Haemagglutinin of H10N8 Influenza Virus Isolated from Humans in Complex with Human Receptor Analogue 6'SLN | |||||||||
Components | (HAEMAGGLUTININ ...) x 2 | |||||||||
Keywords | VIRAL PROTEIN / H10N8 / INFLUENZA / SIALIC ACID / GLYCOPROTEIN / VIRUS RECEPTOR / AVIAN FLU / SIALYLLACTOSAMINE / LSTA | |||||||||
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 / 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 VIRUS A/JIANGXI- DONGHU/346/2013 | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Xiong, X. / Haire, L.F. / Vachieri, S.G. / Collins, P.J. / Walker, P.A. / Martin, S.R. / Zhang, Y. / McCauley, J.W. / Gamblin, S.J. / Skehel, J.J. | |||||||||
Citation | Journal: Nature / Year: 2014 Title: Receptor Binding by H10 Influenza Viruses. Authors: Vachieri, S.G. / Xiong, X. / Collins, P.J. / Walker, P.A. / Martin, S.R. / Haire, L.F. / Zhang, Y. / Mccauley, J.W. / Gamblin, S.J. / Skehel, J.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4d00.cif.gz | 581.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d00.ent.gz | 487.8 KB | Display | PDB format |
PDBx/mmJSON format | 4d00.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4d00_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 4d00_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 4d00_validation.xml.gz | 59.6 KB | Display | |
Data in CIF | 4d00_validation.cif.gz | 84.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/4d00 ftp://data.pdbj.org/pub/pdb/validation_reports/d0/4d00 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-HAEMAGGLUTININ ... , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 35682.258 Da / Num. of mol.: 3 Fragment: HA1 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES -2-323 Source method: isolated from a genetically manipulated source Source: (gene. exp.) INFLUENZA VIRUS A/JIANGXI- DONGHU/346/2013 (H10N8) Description: CHINA CDC / Plasmid: PFASTBAC1 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q0A448*PLUS #2: Protein | Mass: 20921.969 Da / Num. of mol.: 3 Fragment: HA2 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 1-183 Source method: isolated from a genetically manipulated source Source: (gene. exp.) INFLUENZA VIRUS A/JIANGXI- DONGHU/346/2013 (H10N8) Description: CHINA CDC / Plasmid: PFASTBAC1 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P12581*PLUS |
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-Sugars , 3 types, 12 molecules
#3: Polysaccharide | #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / |
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-Non-polymers , 2 types, 706 molecules
#6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE GLOBAL INITIATIVE |
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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: 4.02 Å3/Da / Density % sol: 69 % / Description: NONE |
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Crystal grow | Details: 10% PEG 6000, 5% MPD AND 0.1 M HEPES PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 |
Detector | Type: RIGAKU R-AXIS IV |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→40 Å / Num. obs: 390165 / % possible obs: 92.8 % / Observed criterion σ(I): -1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 6.21 |
Reflection shell | Resolution: 2.5→2.61 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.06 / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→132.58 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.896 / SU B: 15.829 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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: 30.987 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→132.58 Å
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Refine LS restraints |
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