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Yorodumi- PDB-5xl3: Complex structure of H4 hemagglutinin from avian influenza H4N6 v... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xl3 | |||||||||
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Title | Complex structure of H4 hemagglutinin from avian influenza H4N6 virus with LSTa | |||||||||
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: 2.203 Å | |||||||||
Authors | Song, H. / Qi, J. / Gao, G.F. | |||||||||
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 | 5xl3.cif.gz | 413.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xl3.ent.gz | 340.6 KB | Display | PDB format |
PDBx/mmJSON format | 5xl3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xl/5xl3 ftp://data.pdbj.org/pub/pdb/validation_reports/xl/5xl3 | HTTPS FTP |
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-Related structure data
Related structure data | 5xl1C 5xl2C 5xl4C 5xl5C 5xl6C 5xl7C 5xl8C 5xl9C 5xlaC 5xlbC 5xlcC 5xldC 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
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 35966.461 Da / Num. of mol.: 2 / Fragment: UNP residues 17-343 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 |
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-Sugars , 3 types, 6 molecules
#3: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 3'-sialyl-N-acetyllactosamine | ||
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#4: Sugar | ChemComp-NAG / #5: Sugar | ChemComp-SIA / | |
-Non-polymers , 1 types, 372 molecules
#6: 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: 8 Details: 0.2 M Trimethylamine N-oxide dehydrate, 0.1 M Tris (pH 8.0), and 20% PEG MME 2000 |
-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: Jul 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 68360 / % possible obs: 99.9 % / Redundancy: 10.3 % / Net I/σ(I): 24.3 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.853 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.853 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HA0 Resolution: 2.203→49.091 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.03
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.203→49.091 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: -105.5024 Å / Origin y: 202.9967 Å / Origin z: 61.3 Å
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Refinement TLS group | Selection details: all |