+Open data
-Basic information
Entry | Database: PDB / ID: 6j1u | ||||||
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Title | influenza virus nucleoprotein with a specific inhibitor | ||||||
Components | Nucleoprotein | ||||||
Keywords | VIRAL PROTEIN / inhibitor / complex / influenza / H1N1 | ||||||
Function / homology | Function and homology information negative stranded viral RNA replication / 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 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Pang, B. / Zhang, W.Z. / Zhang, H.M. / Hao, Q. | ||||||
Citation | Journal: J.Virol. / Year: 2021 Title: Discovery of a Novel Specific Inhibitor Targeting Influenza A Virus Nucleoprotein with Pleiotropic Inhibitory Effects on Various Steps of the Viral Life Cycle. Authors: Yang, F. / Pang, B. / Lai, K.K. / Cheung, N.N. / Dai, J. / Zhang, W. / Zhang, J. / Chan, K.H. / Chen, H. / Sze, K.H. / Zhang, H. / Hao, Q. / Yang, D. / Yuen, K.Y. / Kao, R.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6j1u.cif.gz | 512 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j1u.ent.gz | 423.6 KB | Display | PDB format |
PDBx/mmJSON format | 6j1u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6j1u_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6j1u_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6j1u_validation.xml.gz | 47.9 KB | Display | |
Data in CIF | 6j1u_validation.cif.gz | 65 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j1/6j1u ftp://data.pdbj.org/pub/pdb/validation_reports/j1/6j1u | HTTPS FTP |
-Related structure data
Related structure data | 2iqhS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
#1: Protein | Mass: 56454.793 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (strain A/Wilson-Smith/1933 H1N1) Strain: A/Wilson-Smith/1933 H1N1 / Gene: NP / Production host: Escherichia coli (E. coli) / References: UniProt: Q1K9H2, UniProt: P15682*PLUS #2: Chemical | |
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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: 2.18 Å3/Da / Density % sol: 43.45 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M sodium acetate, 0.05 M magnesium acetate, 0.1 M MES, pH 6.0, 7% PEG8000 and 5% glycerol Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 16, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 39939 / % possible obs: 92.3 % / Redundancy: 6.5 % / Biso Wilson estimate: 51.5 Å2 / Rmerge(I) obs: 0.118 / Net I/av σ(I): 13.9 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.8→2.93 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.04 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 3247 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2IQH Resolution: 2.8→43.53 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.877 / SU B: 31.451 / SU ML: 0.284 / Cross valid method: THROUGHOUT / ESU R Free: 0.416 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.282 Å2
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Refinement step | Cycle: 1 / Resolution: 2.8→43.53 Å
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Refine LS restraints |
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