+Open data
-Basic information
Entry | Database: PDB / ID: 7ulo | ||||||
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Title | Potato leafroll virus N-terminal readthrough domain | ||||||
Components | (Minor capsid protein P3-RTD) x 2 | ||||||
Keywords | VIRAL PROTEIN / Viral transmission / dimer / vector interaction | ||||||
Function / homology | Potato leaf roll virus readthrough protein / Potato leaf roll virus readthrough protein / Luteovirus group 1 coat protein / Luteovirus coat protein / Viral coat protein subunit / viral capsid / structural molecule activity / Readthrough protein / Readthrough protein Function and homology information | ||||||
Biological species | Potato leafroll virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.21 Å | ||||||
Authors | Schiltz, C.J. / Chappie, J.S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Polerovirus N-terminal readthrough domain structures reveal molecular strategies for mitigating virus transmission by aphids Authors: Schiltz, C.J. / Wilson, J.R. / Hosford, C.J. / Adams, M.C. / Preising, S.E. / DeBlasio, S.L. / MacLeod, H.J. / Van Eck, J. / Heck, M.L. / Chappie, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ulo.cif.gz | 114.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ulo.ent.gz | 75.2 KB | Display | PDB format |
PDBx/mmJSON format | 7ulo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ulo_validation.pdf.gz | 453 KB | Display | wwPDB validaton report |
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Full document | 7ulo_full_validation.pdf.gz | 456.4 KB | Display | |
Data in XML | 7ulo_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 7ulo_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ul/7ulo ftp://data.pdbj.org/pub/pdb/validation_reports/ul/7ulo | HTTPS FTP |
-Related structure data
Related structure data | 7ulnC C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 24105.619 Da / Num. of mol.: 2 Fragment: N-terminal readthrough domain (UNP residues 230-436) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Potato leafroll virus / Production host: Escherichia coli (E. coli) / References: UniProt: Q8QYP3 #2: Protein/peptide | | Mass: 2446.726 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 437-458) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Potato leafroll virus / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D5MCF4 #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.23 Å3/Da / Density % sol: 44.78 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris-HCl, pH 8.5, 0.25 M ammonium sulfate, 14% PEG8000, 3% ethylene glycol, 5 mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 21, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.21→65.15 Å / Num. obs: 22427 / % possible obs: 96.8 % / Redundancy: 5.1 % / Biso Wilson estimate: 54.54 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.045 / Rrim(I) all: 0.107 / Net I/σ(I): 10.5 / Num. measured all: 115339 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.21→56.01 Å / SU ML: 0.4485 / Cross valid method: FREE R-VALUE / σ(F): 1.7 / Phase error: 36.1557 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 57.55 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.21→56.01 Å
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Refine LS restraints |
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LS refinement shell |
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