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- EMDB-33168: structure of vp51 in white spot syndrome virus capsid -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-33168
Titlestructure of vp51 in white spot syndrome virus capsid
Map data
Sample
  • Complex: white spot syndrome virus
    • Protein or peptide: Capsid protein
KeywordsComplex / C14 / capsid / disc / VIRAL PROTEIN
Function / homologyviral envelope / DNA binding / Capsid protein
Function and homology information
Biological speciesWhite spot syndrome virus
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 3.73 Å
AuthorsShan H / Liu MD / Shen QT
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870743 China
CitationJournal: To Be Published
Title: structure of vp51 in white spot syndrome virus capsid
Authors: Hong S / Shen QT
History
DepositionMar 31, 2022-
Header (metadata) releaseApr 5, 2023-
Map releaseApr 5, 2023-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33168.png

Downloads & links

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Map

FileDownload / File: emd_33168.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 600 pix.
= 804. Å		1.34 Å/pix.
x 600 pix.
= 804. Å		1.34 Å/pix.
x 600 pix.
= 804. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-0.39552757 - 1.1905851
Average (Standard dev.)0.01599157 (±0.08187125)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 804.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_33168_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_33168_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_33168_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 : white spot syndrome virus

EntireName: white spot syndrome virus
Components
  • Complex: white spot syndrome virus
    • Protein or peptide: Capsid protein

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Supramolecule #1: white spot syndrome virus

SupramoleculeName: white spot syndrome virus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: White spot syndrome virus

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: White spot syndrome virus
Molecular weightTheoretical: 51.965145 KDa
SequenceString: MSASLILDEY LKKTASAVLD VADSFEKIKG EIQSPEEAAA LSVALYGAPP KPSASAVASI ITGERTSLND KYLSDNVLLK MSVARVGQE NNRKRADQAA DEIRTIMEDI TGSLSGAYRQ YSPLEEENKV HIGIMNNKTP SIVCGYYTMD TSISSEPLSL T DFQNPTVI ...String:
MSASLILDEY LKKTASAVLD VADSFEKIKG EIQSPEEAAA LSVALYGAPP KPSASAVASI ITGERTSLND KYLSDNVLLK MSVARVGQE NNRKRADQAA DEIRTIMEDI TGSLSGAYRQ YSPLEEENKV HIGIMNNKTP SIVCGYYTMD TSISSEPLSL T DFQNPTVI ANVTKRMESI FSKVDSARST RFDAFVNGVA NNMDIKSSID WANMVENVIK LPDSTPNPCS VDTIVSRDAS VV KTAVNDI YASVGKSYCR PATQLTFMSE IEKLRKAAVV CFEALMSDTR ERAFVEFLFY VSFKEDASNT NSKLFVQNKL SSM SGNPRQ PIKLVRRSAE ETLFGLCFMF KVMPPEFMNC IFNFPTIPHS TQYHGLYGTC LTPLLRKYGS SFEKSWAHFE EILS ERANA VKKFGVNDTR IDCLDAVANL TGPVYVLILD LVRTLSAQRS CSTKFLREIK ENYLLWNRFV S

UniProtKB: Capsid protein

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
StainingType: NEGATIVE / Material: uranyl acetate
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.25 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 153916
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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