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- EMDB-61714: Local refinement of H14 nanotubes assembled from baculovirus caps... -

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Basic information

Entry
Database: EMDB / ID: EMD-61714
TitleLocal refinement of H14 nanotubes assembled from baculovirus capsid protein
Map data
Sample
  • Complex: H14 nanotubes assembled from HaCP
    • Protein or peptide: Viral capsid 39 protein
Keywordscapsid protein / self-assembly / Baculovirus / nanotube / VIRAL PROTEIN
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
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsTian K / Rao G / Fu Y / Cao S
Funding support China, 1 items
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, 2024-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61714.png

Downloads & links

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Map

FileDownload / File: emd_61714.map.gz / Format: CCP4 / Size: 744.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 580 pix.
= 759.8 Å		1.31 Å/pix.
x 580 pix.
= 759.8 Å		1.31 Å/pix.
x 580 pix.
= 759.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.31 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-3.6456597 - 5.954081
Average (Standard dev.)0.021162374 (±0.07365979)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions580580580
Spacing580580580
CellA=B=C: 759.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61714_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61714_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : H14 nanotubes assembled from HaCP

EntireName: H14 nanotubes assembled from HaCP
Components
  • Complex: H14 nanotubes assembled from HaCP
    • Protein or peptide: Viral capsid 39 protein

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Supramolecule #1: H14 nanotubes assembled from HaCP

SupramoleculeName: H14 nanotubes assembled from HaCP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Helicoverpa armigera nucleopolyhedrovirus

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Macromolecule #1: Viral capsid 39 protein

MacromoleculeName: Viral capsid 39 protein / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Helicoverpa armigera nucleopolyhedrovirus
Molecular weightTheoretical: 33.433945 KDa
SequenceString: MALVTVPTAT TRLRNFCVFS SVKPLDFCDQ YSSPCSSDAT VDDGWFVCEY HASRFFKMEK LALAIPDGTG NNYYRTVGKS LVDDKAEGI ERILIPSQNN YETVLNLSLL GPAERLVFYM IYDNKEKQNE ICQQLRMYER FRPEVVEELY NSTLRVLALT N PDAYCAQT ...String:
MALVTVPTAT TRLRNFCVFS SVKPLDFCDQ YSSPCSSDAT VDDGWFVCEY HASRFFKMEK LALAIPDGTG NNYYRTVGKS LVDDKAEGI ERILIPSQNN YETVLNLSLL GPAERLVFYM IYDNKEKQNE ICQQLRMYER FRPEVVEELY NSTLRVLALT N PDAYCAQT NTNESRSFGL SVEDDLAFNV LPTFIQNLIR KCVAPESLTI GTEDLQLRNC NTCRITSEGL LASVRLYNSV QP KYLYGVN ENRLQIRNVL QFQGNANALQ QKLSRYELYQ INIPLFLGKQ IISTGR

UniProtKB: Viral capsid 39 protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5321708
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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