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- PDB-5h0r: RNA dependent RNA polymerase ,vp4,dsRNA -

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Entry
Database: PDB / ID: 5h0r
TitleRNA dependent RNA polymerase ,vp4,dsRNA
Components
  • (RNA (42-MER)) x 2
  • RNA-dependent RNA polymerase
  • VP4 protein
KeywordsTRANSFERASE/RNA / structural classification / TRANSFERASE-RNA complex
Function / homologyRNA-directed RNA polymerase, reovirus / RdRp of Reoviridae dsRNA viruses catalytic domain profile. / viral genome replication / RNA-directed 5'-3' RNA polymerase activity / RNA binding / RNA-dependent RNA polymerase / VP4 protein
Function and homology information
Specimen sourceBombyx mori cytoplasmic polyhedrosis virus
Dendrolimus punctatus cypovirus 1
Cypovirus (cytoplasmic polyhedrosis viruses)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.9 Å resolution
AuthorsLi, X. / Zhou, N. / Chen, W. / Zhu, B. / Wang, X. / Xu, B. / Wang, J. / Liu, H. / Cheng, L.
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Near-Atomic Resolution Structure Determination of a Cypovirus Capsid and Polymerase Complex Using Cryo-EM at 200kV.
Authors: Xiaowu Li / Niyun Zhou / Wenyuan Chen / Bin Zhu / Xurong Wang / Bin Xu / Jiawei Wang / Hongrong Liu / Lingpeng Cheng
Abstract: Single-particle cryo-electron microscopy (cryo-EM) allows the high-resolution structural determination of biological assemblies in a near-native environment. However, all high-resolution (better than ...Single-particle cryo-electron microscopy (cryo-EM) allows the high-resolution structural determination of biological assemblies in a near-native environment. However, all high-resolution (better than 3.5Å) cryo-EM structures reported to date were obtained by using 300kV transmission electron microscopes (TEMs). We report here the structures of a cypovirus capsid of 750-Å diameter at 3.3-Å resolution and of RNA-dependent RNA polymerase (RdRp) complexes within the capsid at 3.9-Å resolution using a 200-kV TEM. The newly resolved structure revealed conformational changes of two subdomains in the RdRp. These conformational changes, which were involved in RdRp's switch from non-transcribing to transcribing mode, suggest that the RdRp may facilitate the unwinding of genomic double-stranded RNA. The possibility of 3-Å resolution structural determinations for biological assemblies of relatively small sizes using cryo-EM at 200kV was discussed.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 6, 2016 / Release: Jan 25, 2017

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Assembly

Deposited unit
F: RNA-dependent RNA polymerase
G: VP4 protein
H: RNA (42-MER)
I: RNA (42-MER)


Theoretical massNumber of molelcules
Total (without water)229,4084
Polyers229,4084
Non-polymers00
Water0
1
F: RNA-dependent RNA polymerase
H: RNA (42-MER)
I: RNA (42-MER)


Theoretical massNumber of molelcules
Total (without water)165,6733
Polyers165,6733
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
2
G: VP4 protein


Theoretical massNumber of molelcules
Total (without water)63,7351
Polyers63,7351
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide RNA-dependent RNA polymerase /


Mass: 139077.281 Da / Num. of mol.: 1
Source: (gene. exp.) Bombyx mori cytoplasmic polyhedrosis virus
Gene: RdRpRNA-dependent RNA polymerase
Production host: Cypovirus (cytoplasmic polyhedrosis viruses)
References: UniProt: A0A0S1LIW6
#2: Protein/peptide VP4 protein


Mass: 63734.707 Da / Num. of mol.: 1 / Source: (gene. exp.) Dendrolimus punctatus cypovirus 1
Production host: Cypovirus (cytoplasmic polyhedrosis viruses)
References: UniProt: Q80A92
#3: RNA chain RNA (42-MER)


Mass: 13781.683 Da / Num. of mol.: 1
Source: (synth.) Cypovirus (cytoplasmic polyhedrosis viruses)
#4: RNA chain RNA (42-MER)


Mass: 12814.002 Da / Num. of mol.: 1
Source: (synth.) Cypovirus (cytoplasmic polyhedrosis viruses)

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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

Component
IDNameTypeEntity IDParent IDSource
1RNA dependent RNA polymerase ,VP4,dsRNACOMPLEX1, 2, 3, 40MULTIPLE SOURCES
2RNA dependent RNA polymeraseCOMPLEX11RECOMBINANT
3VP4COMPLEX21RECOMBINANT
4dsRNACOMPLEX31MULTIPLE SOURCES
5dsRNACOMPLEX41MULTIPLE SOURCES
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
1110981Cypovirus (cytoplasmic polyhedrosis viruses)
2210981Cypovirus (cytoplasmic polyhedrosis viruses)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 27000 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.02015526
ELECTRON MICROSCOPYf_angle_d0.79021397
ELECTRON MICROSCOPYf_dihedral_angle_d8.47312170
ELECTRON MICROSCOPYf_chiral_restr0.0472465
ELECTRON MICROSCOPYf_plane_restr0.0042425

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