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Yorodumi- PDB-5tjw: Influenza A virus Nucleoprotein in Complex with Inhibitory Nanobody -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tjw | ||||||
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Title | Influenza A virus Nucleoprotein in Complex with Inhibitory Nanobody | ||||||
Components |
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Keywords | Viral Protein/Immune System / Influenza / nucleoprotein / VHH / inhibitory / Viral Protein-Immune System complex | ||||||
Function / homology | Function and homology information helical viral capsid / viral penetration into host nucleus / host cell / viral nucleocapsid / ribonucleoprotein complex / symbiont entry into host cell / host cell nucleus / structural molecule activity / RNA binding / identical protein binding Similarity search - Function | ||||||
Biological species | Influenza A virus Vicugna pacos (alpaca) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.231 Å | ||||||
Authors | Hanke, L. / Knockenhauer, K.E. / Ploegh, H.L. / Schwartz, T.U. | ||||||
Citation | Journal: MBio / Year: 2016 Title: The Antiviral Mechanism of an Influenza A Virus Nucleoprotein-Specific Single-Domain Antibody Fragment. Authors: Hanke, L. / Knockenhauer, K.E. / Brewer, R.C. / van Diest, E. / Schmidt, F.I. / Schwartz, T.U. / Ploegh, H.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tjw.cif.gz | 127.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tjw.ent.gz | 98.2 KB | Display | PDB format |
PDBx/mmJSON format | 5tjw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5tjw_validation.pdf.gz | 434.5 KB | Display | wwPDB validaton report |
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Full document | 5tjw_full_validation.pdf.gz | 442.4 KB | Display | |
Data in XML | 5tjw_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | 5tjw_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tj/5tjw ftp://data.pdbj.org/pub/pdb/validation_reports/tj/5tjw | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Hexamer confirmed by gel filtration |
-Components
#1: Protein | Mass: 57583.012 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/WSN/1933(H1N1)) / Strain: A/WSN/1933(H1N1) / Gene: NP / Plasmid: pet30b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: B4URF1, UniProt: Q1K9H2*PLUS |
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#2: Antibody | Mass: 14934.183 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Plasmid: pHEN-6 / Production host: Escherichia coli (E. coli) / Strain (production host): WK6 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.87 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1 M sodium acetate, 1.5 M ammonium sulfate, 0.025% (v/v) dichloromethane |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9778 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 |
Reflection | Resolution: 3.22→97.26 Å / Num. obs: 14189 / % possible obs: 99 % / Redundancy: 9.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.178 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 3.22→3.34 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 2.1 / CC1/2: 0.687 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2IQH, 4KRL Resolution: 3.231→97.261 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.47 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.231→97.261 Å
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Refine LS restraints |
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LS refinement shell |
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