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Yorodumi- PDB-5xld: The structure of hemagglutinin Q226L-G228S mutant from an avian-o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xld | |||||||||
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Title | The structure of hemagglutinin Q226L-G228S mutant from an avian-origin H4N6 influenza virus in complex with human receptor analog LSTc | |||||||||
Components | (Hemagglutinin) x 2 | |||||||||
Keywords | VIRAL PROTEIN / H4 hemagglutinin / influenza virus / receptor binding | |||||||||
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 / membrane Similarity search - Function | |||||||||
Biological species | Influenza A virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Song, H. / Qi, J. / Gao, F.G. | |||||||||
Citation | Journal: Cell Rep / Year: 2017 Title: Avian-to-Human Receptor-Binding Adaptation by Influenza A Virus Hemagglutinin H4 Authors: Song, H. / Qi, J. / Xiao, H. / Bi, Y. / Zhang, W. / Xu, Y. / Wang, F. / Shi, Y. / Gao, G.F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xld.cif.gz | 410.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xld.ent.gz | 338.8 KB | Display | PDB format |
PDBx/mmJSON format | 5xld.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xld_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 5xld_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5xld_validation.xml.gz | 40.8 KB | Display | |
Data in CIF | 5xld_validation.cif.gz | 56.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xl/5xld ftp://data.pdbj.org/pub/pdb/validation_reports/xl/5xld | HTTPS FTP |
-Related structure data
Related structure data | 5xl1C 5xl2C 5xl3C 5xl4C 5xl5C 5xl6C 5xl7C 5xl8C 5xl9C 5xlaC 5xlbC 5xlcC 1ha0S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 35981.516 Da / Num. of mol.: 2 / Fragment: UNP residues 17-343 / Mutation: Q226L, G228S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (strain A/Duck/Czechoslovakia/1956 H4N6) Strain: A/Duck/Czechoslovakia/1956 H4N6 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A3KF09, UniProt: P19696*PLUS #2: Protein | Mass: 20342.391 Da / Num. of mol.: 2 / Fragment: UNP residues 344-519 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (strain A/Duck/Czechoslovakia/1956 H4N6) Strain: A/Duck/Czechoslovakia/1956 H4N6 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A3KF09, UniProt: P19696*PLUS #3: Polysaccharide | #4: Sugar | ChemComp-NAG / #5: Water | ChemComp-HOH / | |
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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: 2.96 Å3/Da / Density % sol: 58.42 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.1 M MES monohydrate (pH 6.0) and 14% (w/v) PEG 4,000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 31, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 60153 / % possible obs: 99.9 % / Redundancy: 10.3 % / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 4 / Rsym value: 0.689 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HA0 Resolution: 2.3→42.73 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.52
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Bsol: 33.6 Å2 / ksol: 0.33 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.3→42.73 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -72.9665 Å / Origin y: 337.6914 Å / Origin z: 747.6565 Å
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Refinement TLS group | Selection details: ALL |