[English] 日本語
Yorodumi- PDB-6gvy: Mutant M16A of RNA dependent RNA polymerase 3D from Foot-and-Mout... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gvy | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Mutant M16A of RNA dependent RNA polymerase 3D from Foot-and-Mouth disease Virus complexed with an template -primer RNA | |||||||||
Components |
| |||||||||
Keywords | VIRAL PROTEIN / RNA dependent RNA polymerase / Picornavirus / closed right hand conformation | |||||||||
Function / homology | Function and homology information L-peptidase / modulation by virus of host chromatin organization / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / protein complex oligomerization ...L-peptidase / modulation by virus of host chromatin organization / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / regulation of translation / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / induction by virus of host autophagy / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Foot-and-mouth disease virus - type C synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Verdaguer, N. / Ferrer-Orta, C. | |||||||||
Funding support | Spain, 2items
| |||||||||
Citation | Journal: J. Virol. / Year: 2018 Title: Contribution of a Multifunctional Polymerase Region of Foot-and-Mouth Disease Virus to Lethal Mutagenesis. Authors: de la Higuera, I. / Ferrer-Orta, C. / Moreno, E. / de Avila, A.I. / Soria, M.E. / Singh, K. / Caridi, F. / Sobrino, F. / Sarafianos, S.G. / Perales, C. / Verdaguer, N. / Domingo, E. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6gvy.cif.gz | 214.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6gvy.ent.gz | 169.5 KB | Display | PDB format |
PDBx/mmJSON format | 6gvy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gvy_validation.pdf.gz | 471.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6gvy_full_validation.pdf.gz | 475 KB | Display | |
Data in XML | 6gvy_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 6gvy_validation.cif.gz | 25.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/6gvy ftp://data.pdbj.org/pub/pdb/validation_reports/gv/6gvy | HTTPS FTP |
-Related structure data
Related structure data | 6gvvC 1wneS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 54050.219 Da / Num. of mol.: 1 / Mutation: M16A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Foot-and-mouth disease virus - type C / Production host: Escherichia coli (E. coli) / References: UniProt: Q0QEE0, UniProt: P03311*PLUS |
---|---|
#2: RNA chain | Mass: 1601.024 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: RNA chain | Mass: 2517.553 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.93 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 30% PEG 4000, 0.2M magnesium acetate, 0.1M MES[2-(N-morpholino) ethanesulfonic acid] pH 6.0 and 4% butyrolactone. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97947 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97947 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 26375 / % possible obs: 100 % / Redundancy: 4.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.027 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.2→2.32 Å / Num. unique all: 3774 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1wne Resolution: 2.2→42.59 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / SU B: 20.746 / SU ML: 0.232 / Cross valid method: THROUGHOUT / ESU R: 0.355 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 65.444 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.2→42.59 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|