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- PDB-9jpt: Local refinement of H14 nanotubes assembled from baculovirus caps... -

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Basic information

Entry
Database: PDB / ID: 9jpt
TitleLocal refinement of H14 nanotubes assembled from baculovirus capsid protein
ComponentsViral capsid 39 protein
KeywordsVIRAL PROTEIN / capsid protein / self-assembly / Baculovirus / nanotube
Function / homologyBaculovirus major capsid protein VP39 / Baculovirus major capsid protein VP39 / viral capsid / structural molecule activity / Viral capsid 39 protein
Function and homology information
Biological speciesHelicoverpa armigera nucleopolyhedrovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 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: Virol Sin / Year: 2025
Title: Structural polymorphism of two-dimensional lattices assembled from baculoviral capsid proteins.
Authors: Kexing Tian / Heya Na / Yan Fu / Tingting Chong / Chao Leng / Fanxing Meng / Yaozhou Liang / Manli Wang / Zhihong Hu / Xi Wang / Guibo Rao / Sheng Cao /
Abstract: Protein nanotubes (PNTs) can be regarded as two-dimensional (2D) lattices with p1 or p2 symmetry rolled into tubes. However, attempts to re-assemble their building blocks into stable 2D nanomaterials ...Protein nanotubes (PNTs) can be regarded as two-dimensional (2D) lattices with p1 or p2 symmetry rolled into tubes. However, attempts to re-assemble their building blocks into stable 2D nanomaterials often fail. Here, starting from two baculoviral capsid proteins, we screened protein variants for the in vitro assembly of various nanotubes and nanosheets. These high-order assemblies were structurally characterized by cryo-electron microscopy techniques. Interfacial analysis of three groups of PNTs revealed that helical heterogeneity is largely the result of the redundancy of p2 symmetry-related contacting interfaces. The assembled nanosheets showed similar interfacial networks to their nanotubular counterparts. In addition, foreign macromolecules could be efficiently displayed on the size-controllable double-layered nanosheets. This study sheds light on the rational design of flexible nanosheets, and it also provides novel 2D protein scaffolds for developing biocompatible materials.
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
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Revision 1.0Oct 22, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Viral capsid 39 protein
B: Viral capsid 39 protein
C: Viral capsid 39 protein
D: Viral capsid 39 protein
E: Viral capsid 39 protein
F: Viral capsid 39 protein
G: Viral capsid 39 protein
H: Viral capsid 39 protein


Theoretical massNumber of molelcules
Total (without water)267,4728
Polymers267,4728
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
Viral capsid 39 protein / Vp39


Mass: 33433.945 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Helicoverpa armigera nucleopolyhedrovirus / References: UniProt: Q77K63
Has protein modificationY

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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: H14 nanotubes assembled from HaCP / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Helicoverpa armigera nucleopolyhedrovirus
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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5321708 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00218288
ELECTRON MICROSCOPYf_angle_d0.5924792
ELECTRON MICROSCOPYf_dihedral_angle_d5.0562480
ELECTRON MICROSCOPYf_chiral_restr0.0422784
ELECTRON MICROSCOPYf_plane_restr0.0043256

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