+Open data
-Basic information
Entry | Database: PDB / ID: 7v38 | |||||||||
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Title | Crystal structure of NP exonuclease-PCMPS complex | |||||||||
Components | Nucleoprotein | |||||||||
Keywords | VIRAL PROTEIN / DEDDh exonuclease / NP exonuclease / anti-viral drug / PCMPS / PCMB | |||||||||
Function / homology | Function and homology information symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / RNA-templated viral transcription / negative stranded viral RNA replication / helical viral capsid / 3'-5' exonuclease activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / RNA-templated viral transcription / negative stranded viral RNA replication / helical viral capsid / 3'-5' exonuclease activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA binding / identical protein binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Lassa virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.403 Å | |||||||||
Authors | Hsiao, Y.Y. / Huang, K.W. | |||||||||
Funding support | Taiwan, 2items
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Citation | Journal: Jacs Au / Year: 2021 Title: Targeted Covalent Inhibitors Allosterically Deactivate the DEDDh Lassa Fever Virus NP Exonuclease from Alternative Distal Sites. Authors: Huang, K.W. / Chen, J.W. / Hua, T.Y. / Chu, Y.Y. / Chiu, T.Y. / Liu, J.Y. / Tu, C.I. / Hsu, K.C. / Kao, Y.T. / Chu, J.W. / Hsiao, Y.Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7v38.cif.gz | 179.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7v38.ent.gz | 141.4 KB | Display | PDB format |
PDBx/mmJSON format | 7v38.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v3/7v38 ftp://data.pdbj.org/pub/pdb/validation_reports/v3/7v38 | HTTPS FTP |
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-Related structure data
Related structure data | 7v37C 7v39C 7v3aC 7v3bC 7v3cC 4g9zS 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
#1: Protein | Mass: 27693.641 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lassa virus (strain Mouse/Sierra Leone/Josiah/1976) Strain: Mouse/Sierra Leone/Josiah/1976 / Production host: Escherichia coli (E. coli) References: UniProt: P13699, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.36 Å3/Da / Density % sol: 47.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M Sodium malonate pH 6.0, 20% w/v Polyethylene glycol 3,350, 2 mM Sodium p-chloromercuriphenylsulphonate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.99311 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 29, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.99311 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→30 Å / Num. obs: 20856 / % possible obs: 98.9 % / Redundancy: 11.8 % / Biso Wilson estimate: 48.08 Å2 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.025 / Rrim(I) all: 0.089 / Χ2: 1.719 / Net I/σ(I): 10.8 / Num. measured all: 245203 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: 4G9Z Resolution: 2.403→29.793 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.12
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 206.91 Å2 / Biso mean: 64.0597 Å2 / Biso min: 26.27 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.403→29.793 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 64.0319 Å / Origin y: 67.2699 Å / Origin z: 36.6732 Å
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Refinement TLS group |
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