+Open data
-Basic information
Entry | Database: PDB / ID: 4nlp | ||||||
---|---|---|---|---|---|---|---|
Title | Poliovirus Polymerase - C290V Loop Mutant | ||||||
Components | RNA-directed RNA polymerase 3D-POL | ||||||
Keywords | Viral Protein / hydrolase / polymerase / RNA dependent RNA polymerase / RdRP / virus | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid ...symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / induction by virus of host autophagy / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Human poliovirus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Sholders, A.J. / Peersen, O.B. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2014 Title: Distinct conformations of a putative translocation element in poliovirus polymerase. Authors: Sholders, A.J. / Peersen, O.B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4nlp.cif.gz | 112.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4nlp.ent.gz | 85.1 KB | Display | PDB format |
PDBx/mmJSON format | 4nlp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nlp_validation.pdf.gz | 458.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4nlp_full_validation.pdf.gz | 467.4 KB | Display | |
Data in XML | 4nlp_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 4nlp_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nl/4nlp ftp://data.pdbj.org/pub/pdb/validation_reports/nl/4nlp | HTTPS FTP |
-Related structure data
Related structure data | 4nloC 4nlqC 4nlrC 4nlsC 4nltC 4nluC 4nlvC 4nlwC 4nlxC 4nlyC 1ra6S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 52879.863 Da / Num. of mol.: 1 / Mutation: C290V, L446D, R455D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human poliovirus 1 / Strain: Mahoney / Plasmid: pKK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: P03300, RNA-directed RNA polymerase | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-ACY / #3: Chemical | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 5.05 Å3/Da / Density % sol: 75.66 % |
---|---|
Crystal grow | Temperature: 289 K / pH: 7 Details: Grown in sodium acetate, cacodylate, DTT. Transferred to 250 mM sodium acetate, 30% (w/v) PEG-400, 0.1 M cacodylic acid, and 2 mM DTT, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 |
Detector | Type: NOIR-1 / Detector: CCD / Date: May 25, 2005 |
Radiation | Monochromator: DOUBLE FLAT SI CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 53309 / % possible obs: 100 % / Redundancy: 6.77 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 6.55 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 4.5 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RA6 Resolution: 2.2→30 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Bsol: 37.68 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.91 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.21 Å / Total num. of bins used: 50 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|