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Yorodumi- PDB-5w6r: Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza vi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5w6r | ||||||||||||
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Title | Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in complex with cyclic peptide CP141099 (P6) | ||||||||||||
Components |
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Keywords | VIRAL PROTEIN/PEPTIDE / Glycoprotein / Ectodomain / N-glycosylation / VIRAL PROTEIN / VIRAL PROTEIN-PEPTIDE complex | ||||||||||||
Function / homology | Function and homology information Transport of HA trimer, NA tetramer and M2 tetramer from the endoplasmic reticulum to the Golgi Apparatus / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral mRNA Translation ...Transport of HA trimer, NA tetramer and M2 tetramer from the endoplasmic reticulum to the Golgi Apparatus / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral mRNA Translation / viral budding from plasma membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / clathrin-dependent endocytosis of virus by host cell / 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 / extracellular region / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Influenza A virus synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.731 Å | ||||||||||||
Authors | Wilson, I.A. / Kadam, R.U. | ||||||||||||
Funding support | United States, 1items
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Citation | Journal: Science / Year: 2017 Title: Potent peptidic fusion inhibitors of influenza virus. Authors: Kadam, R.U. / Juraszek, J. / Brandenburg, B. / Buyck, C. / Schepens, W.B.G. / Kesteleyn, B. / Stoops, B. / Vreeken, R.J. / Vermond, J. / Goutier, W. / Tang, C. / Vogels, R. / Friesen, R.H.E. ...Authors: Kadam, R.U. / Juraszek, J. / Brandenburg, B. / Buyck, C. / Schepens, W.B.G. / Kesteleyn, B. / Stoops, B. / Vreeken, R.J. / Vermond, J. / Goutier, W. / Tang, C. / Vogels, R. / Friesen, R.H.E. / Goudsmit, J. / van Dongen, M.J.P. / 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 | 5w6r.cif.gz | 418.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w6r.ent.gz | 345.7 KB | Display | PDB format |
PDBx/mmJSON format | 5w6r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5w6r_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 5w6r_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 5w6r_validation.xml.gz | 71.1 KB | Display | |
Data in CIF | 5w6r_validation.cif.gz | 95.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/5w6r ftp://data.pdbj.org/pub/pdb/validation_reports/w6/5w6r | HTTPS FTP |
-Related structure data
Related structure data | 5w5sC 5w5uC 5w6iC 5w6tC 5w6uC 1ru7S C: citing same article (ref.) S: Starting model for refinement |
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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
-Protein , 2 types, 8 molecules ACEGBDFH
#1: Protein | Mass: 36650.293 Da / Num. of mol.: 4 / Fragment: residues 18-343 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/Puerto Rico/8/1934(H1N1)) Strain: A/Puerto Rico/8/1934 H1N1 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P03452 #2: Protein | Mass: 20138.393 Da / Num. of mol.: 4 / Fragment: residues 344-519 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/Puerto Rico/8/1934(H1N1)) Strain: A/Puerto Rico/8/1934 H1N1 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P03452 |
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-Protein/peptide / Non-polymers , 2 types, 106 molecules MONQ
#3: Protein/peptide | Mass: 1558.775 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #6: Water | ChemComp-HOH / | |
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-Sugars , 2 types, 20 molecules
#4: 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 #5: Sugar | ChemComp-NAG / |
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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: 3.29 Å3/Da / Density % sol: 62.61 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: HA: 11 mg/ml 2M sodium chloride 10% w/v PEG 6000 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.73→50 Å / Num. obs: 76045 / % possible obs: 97.3 % / Redundancy: 2.7 % / CC1/2: 0.9 / Rpim(I) all: 0.06 / Rsym value: 0.1 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.73→2.8 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2 / Num. unique obs: 3897 / CC1/2: 0.58 / Rpim(I) all: 0.47 / Rsym value: 0.8 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RU7 Resolution: 2.731→44.338 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.6
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.731→44.338 Å
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Refine LS restraints |
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LS refinement shell |
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