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Open data
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Basic information
Entry | Database: PDB / ID: 6k32 | ||||||
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Title | RdRp complex | ||||||
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![]() | VIRAL PROTEIN/RNA / Cypovirus / Transcription / RNA-dependent RNA polymerase / VIRAL PROTEIN-RNA complex | ||||||
Function / homology | ![]() T=2 icosahedral viral capsid / viral inner capsid / viral genome replication / RNA-dependent RNA polymerase activity / RNA binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
![]() | Li, X.W. | ||||||
![]() | ![]() Title: Structure of RdRps Within a Transcribing dsRNA Virus Provides Insights Into the Mechanisms of RNA Synthesis. Authors: Xiaowu Li / Li Wang / Xurong Wang / Wenyuan Chen / Tao Yang / Jingdong Song / Hongrong Liu / Lingpeng Cheng / ![]() Abstract: RNA-dependent RNA polymerases (RdRps) catalyze RNA synthesis of RNA viruses. During initiation of RNA synthesis, the RdRp catalyzes the formation of the first dinucleotide, acting as primer for ...RNA-dependent RNA polymerases (RdRps) catalyze RNA synthesis of RNA viruses. During initiation of RNA synthesis, the RdRp catalyzes the formation of the first dinucleotide, acting as primer for subsequent processive RNA elongation. Here, we present the structure of the RdRp complexes in the dinucleotide primed state in situ within a transcribing cypovirus under near physiological conditions using cryo-electron microscopy. The 3' end of RNA templates, paired RNA dinucleotide primer, incoming nucleotide, and catalytic divalent cations in the RdRp were resolved at 3.8 Å resolution. The end of the RNA template and the dinucleotide is buttressed by the aromatic tyrosine in a loop from the RdRp bracelet domain. Our structure reveals the interactions between the nucleotide substrates and the conserved residues during the RdRp initiation, and the coordinated structural changes preceding the elongation stage. In addition, it provides the direct evidence for existence of the slow step of the dinucleotide primed state in the viral RdRp transcription. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Download
PDBx/mmCIF format | ![]() | 1.3 MB | Display | ![]() |
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PDB format | ![]() | 1.1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 197.9 KB | Display | |
Data in CIF | ![]() | 306 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9907MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Protein , 5 types, 7 molecules ABCDEFG
#1: Protein | Mass: 137058.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() References: UniProt: D0EZK6 | ||
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#2: Protein | Mass: 63379.449 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() References: UniProt: C7EWL9 | ||
#5: Protein | Mass: 136769.422 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() References: UniProt: D3JWE6, UniProt: Q6TS43*PLUS | ||
#6: Protein | Mass: 135002.609 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() References: UniProt: D3JWE6, UniProt: Q6TS43*PLUS #7: Protein | | Mass: 137422.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() References: UniProt: D3JWE6, UniProt: Q6TS43*PLUS |
-RNA chain , 2 types, 2 molecules tp
#3: RNA chain | Mass: 1507.928 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() |
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#4: RNA chain | Mass: 869.394 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() |
-Non-polymers , 5 types, 6 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/MG7.gif)
![](data/chem/img/DPO.gif)
![](data/chem/img/A2M.gif)
![](data/chem/img/UTP.gif)
![](data/chem/img/MG7.gif)
![](data/chem/img/DPO.gif)
![](data/chem/img/A2M.gif)
![](data/chem/img/UTP.gif)
#8: Chemical | #9: Chemical | ChemComp-MG7 / | #10: Chemical | ChemComp-DPO / | #11: Chemical | ChemComp-A2M / | #12: Chemical | ChemComp-UTP / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Cypovirus / Type: VIRUS / Entity ID: #1-#7 / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Details of virus | Empty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: OTHER |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI ARCTICA |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.13_2998: / Classification: refinement |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 100000 / Symmetry type: POINT |
Refinement | Highest resolution: 3.2 Å |