[English] 日本語
Yorodumi- PDB-8p0b: Thogoto virus polymerase in Mode B conformation and bound to 32-m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8p0b | ||||||
---|---|---|---|---|---|---|---|
Title | Thogoto virus polymerase in Mode B conformation and bound to 32-mer loop promoter RNA | ||||||
Components |
| ||||||
Keywords | VIRAL PROTEIN / Thogoto / viral RNA-dependent RNA polymerase | ||||||
Function / homology | Function and homology information cap snatching / 7-methylguanosine mRNA capping / virion component / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / host cell nucleus / RNA binding Similarity search - Function | ||||||
Biological species | Thogotovirus thogotoense | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.87 Å | ||||||
Authors | Cusack, S. / Kouba, T. | ||||||
Funding support | France, 1items
| ||||||
Citation | Journal: To Be Published Title: Thogoto virus polymerase Authors: Kouba, T. / Cusack, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8p0b.cif.gz | 292.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8p0b.ent.gz | 222.4 KB | Display | PDB format |
PDBx/mmJSON format | 8p0b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p0/8p0b ftp://data.pdbj.org/pub/pdb/validation_reports/p0/8p0b | HTTPS FTP |
---|
-Related structure data
Related structure data | 17332MC 8p0gC 8p0uC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 71551.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thogotovirus thogotoense / Gene: Segment 3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P27194 | ||
---|---|---|---|
#2: Protein | Mass: 81476.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thogotovirus thogotoense / Gene: Segment 2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O41353, RNA-directed RNA polymerase | ||
#3: Protein | Mass: 88172.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thogotovirus thogotoense / Gene: Segment 1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9YNA4 | ||
#4: RNA chain | Mass: 10217.090 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thogotovirus thogotoense Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Thogotovirus RNA-directed RNA polymerase / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
---|---|
Molecular weight | Value: 0.240 MDa / Experimental value: NO |
Source (natural) | Organism: Thogotovirus thogotoense |
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 400 nm |
Image recording | Electron dose: 49 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 114184 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|