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- PDB-9jps: Local refinement of H12 nanotubes assembled from baculovirus caps... -

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Basic information

Entry
Database: PDB / ID: 9jps
TitleLocal refinement of H12 nanotubes assembled from baculovirus capsid protein
ComponentsGlutathione S-transferase class-mu 26 kDa isozyme,Viral capsid 39 protein
KeywordsVIRAL PROTEIN / capsid protein / self-assembly / Baculovirus / nanotube
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / glutathione metabolic process / viral capsid / structural molecule activity
Similarity search - Function
Baculovirus major capsid protein VP39 / Baculovirus major capsid protein VP39 / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. ...Baculovirus major capsid protein VP39 / Baculovirus major capsid protein VP39 / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
Glutathione S-transferase class-mu 26 kDa isozyme / Viral capsid 39 protein
Similarity search - Component
Biological speciesSchistosoma japonicum (invertebrata)
Helicoverpa armigera nucleopolyhedrovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsTian, K. / Rao, G. / Fu, Y. / Cao, S.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC2303300 China
CitationJournal: To Be Published
Title: Local refinement of H12 nanotubes assembled from baculovirus capsid protein
Authors: Tian, K. / Rao, G. / Fu, Y. / Cao, S.
History
DepositionSep 26, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione S-transferase class-mu 26 kDa isozyme,Viral capsid 39 protein
B: Glutathione S-transferase class-mu 26 kDa isozyme,Viral capsid 39 protein
C: Glutathione S-transferase class-mu 26 kDa isozyme,Viral capsid 39 protein
D: Glutathione S-transferase class-mu 26 kDa isozyme,Viral capsid 39 protein
E: Glutathione S-transferase class-mu 26 kDa isozyme,Viral capsid 39 protein
F: Glutathione S-transferase class-mu 26 kDa isozyme,Viral capsid 39 protein
G: Glutathione S-transferase class-mu 26 kDa isozyme,Viral capsid 39 protein
H: Glutathione S-transferase class-mu 26 kDa isozyme,Viral capsid 39 protein


Theoretical massNumber of molelcules
Total (without water)484,3778
Polymers484,3778
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Glutathione S-transferase class-mu 26 kDa isozyme,Viral capsid 39 protein / GST 26 / Sj26 antigen / SjGST / Vp39


Mass: 60547.168 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma japonicum (invertebrata), (gene. exp.) Helicoverpa armigera nucleopolyhedrovirus
Gene: ORF-77, ORF-78 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P08515, UniProt: Q77K63, glutathione transferase
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: H12 nanotubes assembled from HaCP / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Helicoverpa armigera nucleopolyhedrovirus51313
31Schistosoma japonicum (invertebrata)6182
Source (recombinant)Organism: Escherichia coli BL21 (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

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: 1308954 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00217728
ELECTRON MICROSCOPYf_angle_d0.46124008
ELECTRON MICROSCOPYf_dihedral_angle_d3.2472392
ELECTRON MICROSCOPYf_chiral_restr0.042696
ELECTRON MICROSCOPYf_plane_restr0.0033144

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