[English] 日本語
![](img/lk-miru.gif)
- PDB-8psz: Tilapia Lake Virus polymerase in vRNA elongation state with addit... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8psz | ||||||
---|---|---|---|---|---|---|---|
Title | Tilapia Lake Virus polymerase in vRNA elongation state with additional mode B promoter (transcriptase conformation) | ||||||
![]() |
| ||||||
![]() | VIRAL PROTEIN / Viral polymerase | ||||||
Function / homology | RNA-dependent RNA polymerase activity / DNA/RNA polymerase superfamily / Chem-A0I / RNA / RNA (> 10) / Uncharacterized protein / Putative PB1 / RNA-dependent RNA polymerase![]() | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.42 Å | ||||||
![]() | Arragain, B. / Cusack, S. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structural and functional analysis of the minimal orthomyxovirus-like polymerase of Tilapia Lake Virus from the highly diverged Amnoonviridae family. Authors: Benoit Arragain / Martin Pelosse / Albert Thompson / Stephen Cusack / ![]() ![]() Abstract: Tilapia Lake Virus (TiLV), a recently discovered pathogen of tilapia fish, belongs to the Amnoonviridae family from the Articulavirales order. Its ten genome segments have characteristic conserved ...Tilapia Lake Virus (TiLV), a recently discovered pathogen of tilapia fish, belongs to the Amnoonviridae family from the Articulavirales order. Its ten genome segments have characteristic conserved ends and encode proteins with no known homologues, apart from the segment 1, which encodes an orthomyxo-like RNA-dependent-RNA polymerase core subunit. Here we show that segments 1-3 encode respectively the PB1, PB2 and PA-like subunits of an active heterotrimeric polymerase that maintains all domains found in the distantly related influenza polymerase, despite an unprecedented overall size reduction of 40%. Multiple high-resolution cryo-EM structures of TiLV polymerase in pre-initiation, initiation and active elongation states, show how it binds the vRNA and cRNA promoters and performs RNA synthesis, with both transcriptase and replicase configurations being characterised. However, the highly truncated endonuclease-like domain appears inactive and the putative cap-binding domain is autoinhibited, emphasising that many functional aspects of TiLV polymerase remain to be elucidated. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 554.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 451.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 17865MC ![]() 8psnC ![]() 8psoC ![]() 8psqC ![]() 8pssC ![]() 8psuC ![]() 8psxC ![]() 8pt2C ![]() 8pt6C ![]() 8pt7C ![]() 8pthC ![]() 8ptjC ![]() 8qz8C M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 47780.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
---|---|
#2: Protein | Mass: 57179.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Protein | Mass: 53782.141 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-RNA chain , 2 types, 4 molecules VSDP
#4: RNA chain | Mass: 12736.518 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) ![]() #5: RNA chain | | Mass: 6675.037 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
---|
-Non-polymers , 4 types, 115 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/A0I.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/A0I.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | #7: Chemical | ChemComp-A0I / [( | #8: Chemical | #9: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: Tilapia lake virus polymerase / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-
Processing
EM software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 103012 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||
Refine LS restraints |
|