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Yorodumi- PDB-6tz2: In situ structure of BmCPV RNA-dependent RNA polymerase at elonga... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tz2 | |||||||||||||||||||||||||||
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Title | In situ structure of BmCPV RNA-dependent RNA polymerase at elongation state | |||||||||||||||||||||||||||
Components |
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Keywords | VIRAL PROTEIN / TRANSFERASE/RNA / RdRp-RNA complex / Elongation / Transcription Bubble / TRANSFERASE-RNA complex | |||||||||||||||||||||||||||
Function / homology | Function and homology information viral genome replication / RNA-dependent RNA polymerase activity / RNA binding Similarity search - Function | |||||||||||||||||||||||||||
Biological species | Bombyx mori cytoplasmic polyhedrosis virus | |||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||||||||||||||||||||
Authors | Cui, Y.X. / Zhang, Y.N. / Sun, J.C. / Zhou, Z.H. | |||||||||||||||||||||||||||
Funding support | China, United States, 8items
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Citation | Journal: Nat Struct Mol Biol / Year: 2019 Title: Conservative transcription in three steps visualized in a double-stranded RNA virus. Authors: Yanxiang Cui / Yinong Zhang / Kang Zhou / Jingchen Sun / Z Hong Zhou / Abstract: Endogenous RNA transcription characterizes double-stranded RNA (dsRNA) viruses in the Reoviridae, a family that is exemplified by its simple, single-shelled member cytoplasmic polyhedrosis virus (CPV) ...Endogenous RNA transcription characterizes double-stranded RNA (dsRNA) viruses in the Reoviridae, a family that is exemplified by its simple, single-shelled member cytoplasmic polyhedrosis virus (CPV). Because of the lack of in situ structures of the intermediate stages of RNA-dependent RNA polymerase (RdRp) during transcription, it is poorly understood how RdRp detects environmental cues and internal transcriptional states to initiate and coordinate repeated cycles of transcript production inside the capsid. Here, we captured five high-resolution (2.8-3.5 Å) RdRp-RNA in situ structures-representing quiescent, initiation, early elongation, elongation and abortive states-under seven experimental conditions of CPV. We observed the 'Y'-form initial RNA fork in the initiation state and the complete transcription bubble in the elongation state. These structures reveal that de novo RNA transcription involves three major conformational changes during state transitions. Our results support an ouroboros model for endogenous conservative transcription in dsRNA viruses. | |||||||||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6tz2.cif.gz | 355.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tz2.ent.gz | 279 KB | Display | PDB format |
PDBx/mmJSON format | 6tz2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tz2_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6tz2_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6tz2_validation.xml.gz | 49.9 KB | Display | |
Data in CIF | 6tz2_validation.cif.gz | 77.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tz/6tz2 ftp://data.pdbj.org/pub/pdb/validation_reports/tz/6tz2 | HTTPS FTP |
-Related structure data
Related structure data | 20587MC 6ty8C 6ty9C 6tz0C 6tz1C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 139007.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bombyx mori cytoplasmic polyhedrosis virus References: UniProt: Q993A4, RNA-directed RNA polymerase |
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#2: Protein | Mass: 63683.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bombyx mori cytoplasmic polyhedrosis virus References: UniProt: Q9IR43 |
-RNA chain , 3 types, 3 molecules MNT
#3: RNA chain | Mass: 5466.027 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bombyx mori cytoplasmic polyhedrosis virus |
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#4: RNA chain | Mass: 10977.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bombyx mori cytoplasmic polyhedrosis virus |
#5: RNA chain | Mass: 11806.449 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bombyx mori cytoplasmic polyhedrosis virus |
-Non-polymers , 3 types, 4 molecules
#6: Chemical | ChemComp-ATP / |
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#7: Chemical | ChemComp-UTP / |
#8: Chemical |
-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 |
-Sample preparation
Component | Name: Bombyx mori cypovirus 1 / Type: VIRUS / Entity ID: #1-#5 / Source: NATURAL |
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Source (natural) | Organism: Bombyx mori cytoplasmic polyhedrosis virus |
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION |
Natural host | Organism: Bombyx mori |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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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 |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 145954 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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