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- PDB-5h0s: EM Structure of VP1A and VP1B -

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Basic information

Entry
Database: PDB / ID: 5h0s
TitleEM Structure of VP1A and VP1B
ComponentsVP1
KeywordsTRANSFERASE / structural classification
Function / homology: / CPV Capsid shell protein VP1, small protrusion domain / : / Inner layer core protein VP1-like, C-terminal / T=2 icosahedral viral capsid / viral inner capsid / VP1 / Inner capsid protein VP1
Function and homology information
Biological speciesBombyx mori cypovirus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLi, X. / Zhou, N. / Xu, B. / Chen, W. / Zhu, B. / Wang, X. / Wang, J. / Liu, H. / Cheng, L.
Funding support China, 5items
OrganizationGrant numberCountry
the National Research and Development Program of China2016YFA0501103 China
the National Research and Development Program of China2015CB910104 China
the National Natural Science Foundation of China91530321 China
the National Natural Science Foundation of China31570727 China
the National Natural Science Foundation of China31570742 China
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.
History
DepositionOct 6, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.0Jan 25, 2017Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 25, 2017Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 25, 2017Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jan 25, 2017Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 25, 2017Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 25, 2017Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Oct 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 / em_image_scans / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update
Revision 1.2Jun 18, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 18, 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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Assembly

Deposited unit
B: VP1
C: VP1


Theoretical massNumber of molelcules
Total (without water)297,3922
Polymers297,3922
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area4670 Å2
ΔGint-13 kcal/mol
Surface area100150 Å2

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Components

#1: Protein VP1


Mass: 148696.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori cypovirus 1
Production host: Cypovirus (cytoplasmic polyhedrosis viruses)
References: UniProt: D3JWE6, UniProt: Q6TS43*PLUS
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: Cypovirus / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Source (recombinant)Organism: Cypovirus (cytoplasmic polyhedrosis viruses)
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
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
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
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
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00919272
ELECTRON MICROSCOPYf_angle_d1.13626238
ELECTRON MICROSCOPYf_dihedral_angle_d12.19915874
ELECTRON MICROSCOPYf_chiral_restr0.063032
ELECTRON MICROSCOPYf_plane_restr0.0073431

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