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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 / homologyC2H2-type zinc finger / Reovirus RNA-dependent RNA polymerase lambda 3 / RdRp of Reoviridae dsRNA viruses catalytic domain profile. / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 type domain signature. / Reovirus RNA-dependent RNA polymerase lambda 3 / Reovirus minor core protein Mu-2 / Zinc finger C2H2-type / Reovirus minor core protein, Mu-2 / RNA-directed RNA polymerase, reovirus ...C2H2-type zinc finger / Reovirus RNA-dependent RNA polymerase lambda 3 / RdRp of Reoviridae dsRNA viruses catalytic domain profile. / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 type domain signature. / Reovirus RNA-dependent RNA polymerase lambda 3 / Reovirus minor core protein Mu-2 / Zinc finger C2H2-type / Reovirus minor core protein, Mu-2 / RNA-directed RNA polymerase, reovirus / viral genome replication / viral capsid / nucleic acid binding / RNA-directed 5'-3' RNA polymerase activity / viral nucleocapsid / structural molecule activity / RNA binding / Putative core protein NTPase/VP5 / VP3 / VP2
Function and homology information
Specimen sourceGrass carp reovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.8 Å resolution
AuthorsLiu, H. / Fang, Q. / Cheng, L.
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 12, 2018 / Release: Jul 4, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 4, 2018Structure modelrepositoryInitial release
1.1Jul 25, 2018Structure modelData collection / Database referencescitation_citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

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Structure viewerMolecule:
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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
Polyers1,544,10012
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)91820
ΔGint (kcal/M)-393
Surface area (Å2)434030

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Components

#1: Protein/peptide
VP3


Mass: 132203.312 Da / Num. of mol.: 10 / Source: (gene. exp.) Grass carp reovirus / Production host: Ctenopharyngodon idella (grass carp) / References: UniProt: Q9E3V8
#2: Protein/peptide VP2


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


Mass: 80381.516 Da / Num. of mol.: 1 / Source: (gene. exp.) Grass carp reovirus / Production host: Ctenopharyngodon idella (grass carp) / References: UniProt: Q8JU68

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Grass carp reovirus / Type: VIRUS / Entity ID: 1,2,3 / Source: RECOMBINANT
Source (natural)Organism: Grass carp reovirus
Source (recombinant)Organism: Ctenopharyngodon idella (grass carp)
Details of virusEmpty: NO / Enveloped: NO / Virus isolate: STRAIN / Virus 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
MicroscopyMicroscope model: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / C2 aperture diameter: 70 mm
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
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number 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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