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- EMDB-61997: Local refinement of A7 nanotubes assembled from baculovirus capsi... -

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Basic information

Entry
Database: EMDB / ID: EMD-61997
TitleLocal refinement of A7 nanotubes assembled from baculovirus capsid protein
Map data
Sample
  • Complex: A7 nanotubes assembled from VP39
    • Protein or peptide: Glutathione S-transferase class-mu 26 kDa isozyme,Major capsid protein
Keywordscapsid protein / self-assembly / Baculovirus / nanotube / VIRAL PROTEIN
Function / homology
Function and homology information


host cell nuclear matrix / glutathione transferase / glutathione transferase activity / glutathione metabolic process / virion component / 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 / Major capsid protein
Similarity search - Component
Biological speciesAutographa californica nuclear polyhedrosis virus
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
DepositionOct 17, 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_61997.png

Downloads & links

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Map

FileDownload / File: emd_61997.map.gz / Format: CCP4 / Size: 744.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.31 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.42
Minimum - Maximum-2.5979254 - 4.372728
Average (Standard dev.)0.008469182 (±0.07234284)
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_61997_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61997_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : A7 nanotubes assembled from VP39

EntireName: A7 nanotubes assembled from VP39
Components
  • Complex: A7 nanotubes assembled from VP39
    • Protein or peptide: Glutathione S-transferase class-mu 26 kDa isozyme,Major capsid protein

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Supramolecule #1: A7 nanotubes assembled from VP39

SupramoleculeName: A7 nanotubes assembled from VP39 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Autographa californica nuclear polyhedrosis virus

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Macromolecule #1: Glutathione S-transferase class-mu 26 kDa isozyme,Major capsid protein

MacromoleculeName: Glutathione S-transferase class-mu 26 kDa isozyme,Major capsid protein
type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: glutathione transferase
Source (natural)Organism: Autographa californica nuclear polyhedrosis virus
Molecular weightTheoretical: 69.517164 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MSPILGYWKI KGLVQPTRLL LEYLEEKYEE HLYERDEGDK WRNKKFELGL EFPNLPYYID GDVKLTQSMA IIRYIADKHN MLGGCPKER AEISMLEGAV LDIRYGVSRI AYSKDFETLK VDFLSKLPEM LKMFEDRLCH KTYLNGDHVT HPDFMLYDAL D VVLYMDPM ...String:
MSPILGYWKI KGLVQPTRLL LEYLEEKYEE HLYERDEGDK WRNKKFELGL EFPNLPYYID GDVKLTQSMA IIRYIADKHN MLGGCPKER AEISMLEGAV LDIRYGVSRI AYSKDFETLK VDFLSKLPEM LKMFEDRLCH KTYLNGDHVT HPDFMLYDAL D VVLYMDPM CLDAFPKLVC FKKRIEAIPQ IDKYLKSSKY IAWPLQGWQA TFGGGDHPPK SDLEVLFQGP LGSMALVPVG MA PRQMRVN RCIFASIVSF DACITYKSPC SPDAYHDDGW FICNNHLIKR FKMSKMVLPI FDEDDNQFKM TIARHLVGNK ERG IKRILI PSATNYQDVF NLNSMMQAEQ LIFHLIYNNE NAVNTICDNL KYTEGFTSNT QRVIHSVYAT TKSILDTTNP NTFC SRVSA DELRFFDVTN ARALRGGAGD QLFNNYSGFL QNLIRRAVAP EYLQIDTEEL RFRNCATCII DETGLVASVP DGPEL YNPI RSSDIMRSQP NRLQIRNVLK FEGDTRELDR TLSGYEEYPT YVPLFLGYQI INSENNFLRN DFIPRANPNA TLGGGA VAG PAPGVAGEAG GGIAVGGGGS GGGGSHHHHH HGGSGSSGGG GSSAHIVMVD AYKPTK

UniProtKB: Glutathione S-transferase class-mu 26 kDa isozyme, Major capsid 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: 3402546
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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