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- PDB-3ja4: RNA-dependent RNA polymerases of transcribing cypoviruses -

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Basic information

Entry
Database: PDB / ID: 3ja4
TitleRNA-dependent RNA polymerases of transcribing cypoviruses
ComponentsRNA-dependent RNA polymerase
KeywordsTRANSFERASE / RNA-dependent RNA polymerases / transcribing cypoviruses / icosahedral virus
Function / homology
Function and homology information


viral genome replication / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / RNA binding
Similarity search - Function
: / : / CPV, RNA-directed RNA polymerase, N-terminal / CPV, RNA-directed RNA polymerase, central polymerase domain / CPV, RNA-directed RNA polymerase, C-terminal / RNA-directed RNA polymerase, reovirus / RdRp of Reoviridae dsRNA viruses catalytic domain profile.
Similarity search - Domain/homology
RNA-directed RNA polymerase
Similarity search - Component
Biological speciesBombyx mori cypovirus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsLiu, H. / Cheng, L.
CitationJournal: Science / Year: 2015
Title: Cryo-EM shows the polymerase structures and a nonspooled genome within a dsRNA virus.
Authors: Hongrong Liu / Lingpeng Cheng /
Abstract: Double-stranded RNA (dsRNA) viruses possess a segmented dsRNA genome and a number of RNA-dependent RNA polymerases (RdRps) enclosed in a capsid. Until now, the precise structures of genomes and RdRps ...Double-stranded RNA (dsRNA) viruses possess a segmented dsRNA genome and a number of RNA-dependent RNA polymerases (RdRps) enclosed in a capsid. Until now, the precise structures of genomes and RdRps within the capsids have been unknown. Here we report the structures of RdRps and associated RNAs within nontranscribing and transcribing cypoviruses (NCPV and TCPV, respectively), using a combination of cryo-electron microscopy (cryo-EM) and a symmetry-mismatch reconstruction method. The RdRps and associated RNAs appear to exhibit a pseudo-D3 symmetric organization in both NCPV and TCPV. However, the molecular interactions between RdRps and the genomic RNA were found to differ in these states. Our work provides insight into the mechanisms of the replication and transcription in dsRNA viruses and paves a way for structural determination of lower-symmetry complexes enclosed in higher-symmetry structures.
History
DepositionApr 20, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Other / Category: cell / database_2 / em_image_scans / Item: _cell.length_a / _cell.length_b / _cell.length_c
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • Biological unit as complete point assembly
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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
A: RNA-dependent RNA polymerase


Theoretical massNumber of molelcules
Total (without water)138,8301
Polymers138,8301
Non-polymers00
Water00
1
A: RNA-dependent RNA polymerase
x 6


  • complete point assembly
  • 6-MERIC
  • 833 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)832,9816
Polymers832,9816
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: D3 (2x3 fold dihedral))

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Components

#1: Protein RNA-dependent RNA polymerase / Coordinate model: Cα atoms only


Mass: 138830.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bombyx mori cypovirus 1 / References: UniProt: Q6RJR5

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: transcribing cypoviruses / Type: VIRUS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Oct 10, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 3 nm / Nominal defocus min: 1 nm
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k)

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Processing

SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: Symmetry-mismatch reconstruction of icosahedral virus
Resolution: 4.8 Å / Num. of particles: 36000 / Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms1068 0 0 0 1068

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