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- EMDB-20083: Cryo-EM reconstruction of Sulfolobus polyhedral virus 1 (SPV1) -

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Basic information

Entry
Database: EMDB / ID: EMD-20083
TitleCryo-EM reconstruction of Sulfolobus polyhedral virus 1 (SPV1)
Map dataCryo-EM reconstruction of Sulfolobus polyhedral virus 1 (SPV1)
Sample
  • Virus: Sulfolobus spindle-shaped virus 1
    • Protein or peptide: Structural protein VP4
    • Protein or peptide: Uncharacterized protein
Keywordsarchaeal pilus / STRUCTURAL PROTEIN / icosahedral symmetry / VIRUS
Function / homologyicosahedral viral capsid / Capsid protein VP10 / Capsid protein VP4
Function and homology information
Biological speciesSulfolobus polyhedral virus 1 / Sulfolobus spindle-shaped virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWang F / Liu Y
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122510 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2019
Title: A packing for A-form DNA in an icosahedral virus.
Authors: Fengbin Wang / Ying Liu / Zhangli Su / Tomasz Osinski / Guilherme A P de Oliveira / James F Conway / Stefan Schouten / Mart Krupovic / David Prangishvili / Edward H Egelman /
Abstract: Studies on viruses infecting archaea living in the most extreme environments continue to show a remarkable diversity of structures, suggesting that the sampling continues to be very sparse. We have ...Studies on viruses infecting archaea living in the most extreme environments continue to show a remarkable diversity of structures, suggesting that the sampling continues to be very sparse. We have used electron cryo-microscopy to study at 3.7-Å resolution the structure of the polyhedral virus 1 (SPV1), which was originally isolated from a hot, acidic spring in Beppu, Japan. The 2 capsid proteins with variant single jelly-roll folds form pentamers and hexamers which assemble into a = 43 icosahedral shell. In contrast to tailed icosahedral double-stranded DNA (dsDNA) viruses infecting bacteria and archaea, and herpesviruses infecting animals and humans, where naked DNA is packed under very high pressure due to the repulsion between adjacent layers of DNA, the circular dsDNA in SPV1 is fully covered with a viral protein forming a nucleoprotein filament with attractive interactions between layers. Most strikingly, we have been able to show that the DNA is in an A-form, as it is in the filamentous viruses infecting hyperthermophilic acidophiles. Previous studies have suggested that DNA is in the B-form in bacteriophages, and our study is a direct visualization of the structure of DNA in an icosahedral virus.
History
DepositionApr 10, 2019-
Header (metadata) releaseMay 22, 2019-
Map releaseOct 2, 2019-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6oj0
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6oj0
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20083.png

Downloads & links

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Map

FileDownload / File: emd_20083.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM reconstruction of Sulfolobus polyhedral virus 1 (SPV1)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 800 pix.
= 1120. Å		1.4 Å/pix.
x 800 pix.
= 1120. Å		1.4 Å/pix.
x 800 pix.
= 1120. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.083773166 - 0.18807147
Average (Standard dev.)-0.00016244754 (±0.011951737)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 1120.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z800800800
origin x/y/z0.0000.0000.000
length x/y/z1120.0001120.0001120.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS800800800
D min/max/mean-0.0840.188-0.000

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Supplemental data

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Sample components

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Entire : Sulfolobus spindle-shaped virus 1

EntireName: Sulfolobus spindle-shaped virus 1
Components
  • Virus: Sulfolobus spindle-shaped virus 1
    • Protein or peptide: Structural protein VP4
    • Protein or peptide: Uncharacterized protein

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Supramolecule #1: Sulfolobus spindle-shaped virus 1

SupramoleculeName: Sulfolobus spindle-shaped virus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 244589 / Sci species name: Sulfolobus spindle-shaped virus 1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Sulfolobus sp. S38A

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Macromolecule #1: Structural protein VP4

MacromoleculeName: Structural protein VP4 / type: protein_or_peptide / ID: 1 / Number of copies: 42 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus polyhedral virus 1
Molecular weightTheoretical: 19.394885 KDa
SequenceString:
MSESVTQQVF NFAVTKSQPF GGYVYSTNLT ASTSSAVTST QLTPLNLSIT LGQITLSGNS LVIPATQIWY LTDAYVSVPD YTNITNGAE ADGVILIYKD GVKLMLTTPL ISSMSISNPA RTHLAQAVKY SPQSILTMYF NPTKPATAST SYPNTVYFTV V VVDFSYAQ NPARAVVSAN AVM

UniProtKB: Capsid protein VP4

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Macromolecule #2: Uncharacterized protein

MacromoleculeName: Uncharacterized protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus polyhedral virus 1
Molecular weightTheoretical: 20.617277 KDa
SequenceString:
MLSLDNYSYV HNITTQTNID LSSQQTIHLA SINGKGYIIF LRFFCEGSSA CFTNVKFSVK ANGLVLYSFR YIQLLELGQA IATAIPSSS QGFSTLLSNY NVLISSPIGT LPQLTLYDSY DNRYGAMLQP AFPLPFVNTL SLDVDILPVS QSSYDPIPYS L NDNQISTN APTGKGNISI EYLLYNCLV

UniProtKB: Capsid protein VP10

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 4
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
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 / Details: sphere
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: OTHER / Software - Name: RELION / Details: d99, model:map FSC (0.38), map:map FSC (0.143) / Number images used: 19092
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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