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- PDB-5zvs: Structure of RNA polymerase complex and genome within a dsRNA vir... -

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Basic information

Entry
Database: PDB / ID: 5zvs
TitleStructure of RNA polymerase complex and genome within a dsRNA virus provides insights into the mechanisms of transcription and assembly
Components
  • Putative core protein NTPase/VP5
  • VP2
  • VP3
KeywordsVIRAL PROTEIN / icosahedral capsid / symmetry-mismatch / genome / RNA-dependent RNA polymerase
Function / homology
Function and homology information


viral inner capsid / host cytoskeleton / 7-methylguanosine mRNA capping / viral genome replication / viral capsid / viral nucleocapsid / host cell cytoplasm / RNA helicase activity / hydrolase activity / RNA helicase ...viral inner capsid / host cytoskeleton / 7-methylguanosine mRNA capping / viral genome replication / viral capsid / viral nucleocapsid / host cell cytoplasm / RNA helicase activity / hydrolase activity / RNA helicase / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / structural molecule activity / RNA binding / metal ion binding
Similarity search - Function
RNA-directed RNA polymerase lambda-3 / RNA-directed RNA polymerase lambda-3 / Reovirus minor core protein, Mu-2 / Reovirus minor core protein Mu-2 / Reovirus RNA-dependent RNA polymerase lambda 3 / Reovirus RNA-dependent RNA polymerase lambda 3 / Inner capsid protein lambda-1/ VP3 / C2H2-type zinc finger / RNA-directed RNA polymerase, reovirus / RdRp of Reoviridae dsRNA viruses catalytic domain profile. ...RNA-directed RNA polymerase lambda-3 / RNA-directed RNA polymerase lambda-3 / Reovirus minor core protein, Mu-2 / Reovirus minor core protein Mu-2 / Reovirus RNA-dependent RNA polymerase lambda 3 / Reovirus RNA-dependent RNA polymerase lambda 3 / Inner capsid protein lambda-1/ VP3 / C2H2-type zinc finger / RNA-directed RNA polymerase, reovirus / RdRp of Reoviridae dsRNA viruses catalytic domain profile. / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / DNA/RNA polymerase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Putative core protein NTPase/VP5 / RNA helicase / RNA-directed RNA polymerase
Similarity search - Component
Biological speciesGrass carp reovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLiu, H. / Fang, Q. / Cheng, L.
Funding support China, 5items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0501100 China
Ministry of Science and Technology (China)2015CB910104 China
National Natural Science Foundation of China91530321 China
National Natural Science Foundation of China31672693 China
National Natural Science Foundation of China31570727 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2018
Title: Structure of RNA polymerase complex and genome within a dsRNA virus provides insights into the mechanisms of transcription and assembly.
Authors: Xurong Wang / Fuxian Zhang / Rui Su / Xiaowu Li / Wenyuan Chen / Qingxiu Chen / Tao Yang / Jiawei Wang / Hongrong Liu / Qin Fang / Lingpeng Cheng /
Abstract: Most double-stranded RNA (dsRNA) viruses transcribe RNA plus strands within a common innermost capsid shell. This process requires coordinated efforts by RNA-dependent RNA polymerase (RdRp) together ...Most double-stranded RNA (dsRNA) viruses transcribe RNA plus strands within a common innermost capsid shell. This process requires coordinated efforts by RNA-dependent RNA polymerase (RdRp) together with other capsid proteins and genomic RNA. Here we report the near-atomic resolution structure of the RdRp protein VP2 in complex with its cofactor protein VP4 and genomic RNA within an aquareovirus capsid using 200-kV cryoelectron microscopy and symmetry-mismatch reconstruction. The structure of these capsid proteins enabled us to observe the elaborate nonicosahedral structure within the double-layered icosahedral capsid. Our structure shows that the RdRp complex is anchored at the inner surface of the capsid shell and interacts with genomic dsRNA and four of the five asymmetrically arranged N termini of the capsid shell proteins under the fivefold axis, implying roles for these N termini in virus assembly. The binding site of the RNA end at VP2 is different from the RNA cap binding site identified in the crystal structure of orthoreovirus RdRp λ3, although the structures of VP2 and λ3 are almost identical. A loop, which was thought to separate the RNA template and transcript, interacts with an apical domain of the capsid shell protein, suggesting a mechanism for regulating RdRp replication and transcription. A conserved nucleoside triphosphate binding site was localized in our RdRp cofactor protein VP4 structure, and interactions between the VP4 and the genomic RNA were identified.
History
DepositionMay 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.0Jul 4, 2018Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 4, 2018Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.0Jul 4, 2018Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 4, 2018Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
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Revision 1.0Jul 4, 2018Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation
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Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update
Revision 1.3Jul 2, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

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Assembly

Deposited unit
A: VP3
B: VP3
D: VP3
C: VP3
E: VP3
F: VP3
G: VP3
H: VP3
I: VP3
J: VP3
2: VP2
4: Putative core protein NTPase/VP5


Theoretical massNumber of molelcules
Total (without water)1,544,10012
Polymers1,544,10012
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area91820 Å2
ΔGint-393 kcal/mol
Surface area434030 Å2

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Components

#1: Protein
VP3


Mass: 132203.312 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Grass carp reovirus / Production host: Ctenopharyngodon idella (grass carp) / References: UniProt: Q9E3V8
#2: Protein VP2


Mass: 141685.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Grass carp reovirus / Production host: Ctenopharyngodon idella (grass carp) / References: UniProt: Q9E3V9
#3: Protein Putative core protein NTPase/VP5 / cofactor protein of RNA-dependent RNA polymerase


Mass: 80381.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Grass carp reovirus / Production host: Ctenopharyngodon idella (grass carp) / References: UniProt: Q8JU68
Has protein modificationY

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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: Grass carp reovirus / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Grass carp reovirus
Source (recombinant)Organism: Ctenopharyngodon idella (grass carp)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Image recordingElectron dose: 25 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.008101802
ELECTRON MICROSCOPYf_angle_d0.878139478
ELECTRON MICROSCOPYf_dihedral_angle_d15.00961378
ELECTRON MICROSCOPYf_chiral_restr0.05416235
ELECTRON MICROSCOPYf_plane_restr0.00918125

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