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Yorodumi- PDB-6cf7: Crystal structure of the A/Solomon Islands/3/2006(H1N1) influenza... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cf7 | |||||||||
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Title | Crystal structure of the A/Solomon Islands/3/2006(H1N1) influenza virus hemagglutinin in complex with small molecule JNJ4796 | |||||||||
Components | (Hemagglutinin) x 2 | |||||||||
Keywords | VIRAL PROTEIN / Glycoprotein / Ectodomain / N-glycosylation | |||||||||
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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.719 Å | |||||||||
Authors | Kadam, R.U. / Wilson, I.A. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Science / Year: 2019 Title: A small-molecule fusion inhibitor of influenza virus is orally active in mice. Authors: van Dongen, M.J.P. / Kadam, R.U. / Juraszek, J. / Lawson, E. / Brandenburg, B. / Schmitz, F. / Schepens, W.B.G. / Stoops, B. / van Diepen, H.A. / Jongeneelen, M. / Tang, C. / Vermond, J. / ...Authors: van Dongen, M.J.P. / Kadam, R.U. / Juraszek, J. / Lawson, E. / Brandenburg, B. / Schmitz, F. / Schepens, W.B.G. / Stoops, B. / van Diepen, H.A. / Jongeneelen, M. / Tang, C. / Vermond, J. / van Eijgen-Obregoso Real, A. / Blokland, S. / Garg, D. / Yu, W. / Goutier, W. / Lanckacker, E. / Klap, J.M. / Peeters, D.C.G. / Wu, J. / Buyck, C. / Jonckers, T.H.M. / Roymans, D. / Roevens, P. / Vogels, R. / Koudstaal, W. / Friesen, R.H.E. / Raboisson, P. / Dhanak, D. / Goudsmit, J. / Wilson, I.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cf7.cif.gz | 227.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cf7.ent.gz | 181.6 KB | Display | PDB format |
PDBx/mmJSON format | 6cf7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cf/6cf7 ftp://data.pdbj.org/pub/pdb/validation_reports/cf/6cf7 | HTTPS FTP |
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-Related structure data
Related structure data | 6cfgC 5w5sS 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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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 36423.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A7Y8I1 |
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#2: Protein | Mass: 19956.131 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/Solomon Islands/3/2006(H1N1)) Strain: A/Hong Kong/65446/2008(H1N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: F2NZB4 |
-Sugars , 4 types, 5 molecules
#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | ||
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#4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | ||
#5: Polysaccharide | #6: Sugar | ChemComp-NAG / | |
-Non-polymers , 2 types, 53 molecules
#7: Chemical | ChemComp-EZ7 / |
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#8: 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: 3.11 Å3/Da / Density % sol: 60.45 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2M disodium hydrogen phosphate, 20% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.719→50 Å / Num. obs: 19893 / % possible obs: 99.6 % / Redundancy: 12.4 % / Biso Wilson estimate: 59 Å2 / CC1/2: 0.97 / Rpim(I) all: 0.03 / Rsym value: 0.1 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 2.72→2.77 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 967 / CC1/2: 0.84 / Rpim(I) all: 0.24 / Rsym value: 0.89 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5W5S Resolution: 2.719→44.777 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.9
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.719→44.777 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: 2.2751 Å / Origin y: 27.7487 Å / Origin z: 11.7739 Å
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Refinement TLS group | Selection details: all |