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Yorodumi- PDB-7xiv: Structural insight into the interactions between Lloviu virus VP3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xiv | ||||||||||||||||||
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Title | Structural insight into the interactions between Lloviu virus VP30 and nucleoprotein | ||||||||||||||||||
Components | Nucleocapsid protein,Minor nucleoprotein VP30Capsid | ||||||||||||||||||
Keywords | VIRUS / Lloviu virus / VP30 / NP / Interaction | ||||||||||||||||||
Function / homology | Function and homology information viral RNA genome packaging / viral nucleocapsid / host cell cytoplasm / RNA binding / zinc ion binding / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Lloviu cuevavirus | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.498 Å | ||||||||||||||||||
Authors | Dong, S.S. / Qin, X.C. / Sun, W.Y. / Luan, F.C. / Wang, J.J. / Ma, L. / Li, X.X. / Yang, G.X. / Hao, C.Y. | ||||||||||||||||||
Funding support | China, 5items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2022 Title: Structural insights into the interactions between lloviu virus VP30 and nucleoprotein. Authors: Sun, W. / Luan, F. / Wang, J. / Ma, L. / Li, X. / Yang, G. / Hao, C. / Qin, X. / Dong, S. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xiv.cif.gz | 64.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xiv.ent.gz | 46.1 KB | Display | PDB format |
PDBx/mmJSON format | 7xiv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xi/7xiv ftp://data.pdbj.org/pub/pdb/validation_reports/xi/7xiv | HTTPS FTP |
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-Related structure data
Related structure data | 5dvwS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 19369.811 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lloviu cuevavirus / Strain: isolate Bat/Spain/Asturias-Bat86/2003 / Production host: Expression vector pET-mod (others) / References: UniProt: G8EFI1, UniProt: G8EFI6 #2: Water | ChemComp-HOH / | |
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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: 2.34 Å3/Da / Density % sol: 47.47 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris-HCl, pH 7.0, 0.25 M NaCl, 22% (w/v) polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 13, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.498→32.126 Å / Num. obs: 13571 / % possible obs: 100 % / Redundancy: 13.8 % / Rpim(I) all: 0.02 / Net I/σ(I): 40.4 |
Reflection shell | Resolution: 2.498→2.598 Å / Num. unique obs: 660 / Rpim(I) all: 0.084 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DVW Resolution: 2.498→32.126 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 32.69 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.15 Å2 / Biso mean: 63.953 Å2 / Biso min: 36 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.498→32.126 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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