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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: To Be Published
Title: Local refinement of H14 nanotubes assembled from baculovirus capsid protein
Authors: Tian K / Rao G / Fu Y / Cao S
History
DepositionSep 26, 2024-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing 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
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: 0.4
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

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61714_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

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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