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- EMDB-33148: Tail structure of bacteriophage SSV19 -

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Basic information

Entry
Database: EMDB / ID: EMD-33148
TitleTail structure of bacteriophage SSV19
Map data
Sample
  • Virus: Sulfolobus spindle-shaped virus
    • Protein or peptide: VP1
    • Protein or peptide: C131
    • Protein or peptide: B210
    • Protein or peptide: VP4
KeywordsComplex / VIRAL PROTEIN
Function / homology
Function and homology information


carbohydrate metabolic process / structural molecule activity / membrane
Similarity search - Function
Structural protein VP1/VP3 / Structural protein VP1/VP3 / Family of unknown function / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
VP4 / Uncharacterized protein / Uncharacterized protein / VP1
Similarity search - Component
Biological speciesSulfolobus spindle-shaped virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLiu HR / Chen WY
Funding support China, 5 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)31970170 China
National Natural Science Foundation of China (NSFC)91951000 China
National Natural Science Foundation of China (NSFC)32071209 China
National Natural Science Foundation of China (NSFC)31971122 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Structural insights into a spindle-shaped archaeal virus with a sevenfold symmetrical tail.
Authors: Zhen Han / Wanjuan Yuan / Hao Xiao / Li Wang / Junxia Zhang / Yuning Peng / Lingpeng Cheng / Hongrong Liu / Li Huang /
Abstract: Archaeal viruses with a spindle-shaped virion are abundant and widespread in extremely diverse environments. However, efforts to obtain the high-resolution structure of a spindle-shaped virus have ...Archaeal viruses with a spindle-shaped virion are abundant and widespread in extremely diverse environments. However, efforts to obtain the high-resolution structure of a spindle-shaped virus have been unsuccessful. Here, we present the structure of SSV19, a spindle-shaped virus infecting the hyperthermophilic archaeon sp. E11-6. Our near-atomic structure reveals an unusual sevenfold symmetrical virus tail consisting of the tailspike, nozzle, and adaptor proteins. The spindle-shaped capsid shell is formed by seven left-handed helical strands, constructed of the hydrophobic major capsid protein, emanating from the highly glycosylated tail assembly. Sliding between adjacent strands is responsible for the variation of a virion in size. Ultrathin sections of the SSV19-infected cells show that SSV19 virions adsorb to the host cell membrane through the tail after penetrating the S-layer. The tailspike harbors a putative endo-mannanase domain, which shares structural similarity to a endo-mannanase. Molecules of glycerol dibiphytanyl glycerol tetraether lipid were observed in hydrophobic clefts between the tail and the capsid shell. The nozzle protein resembles the stem and clip domains of the portals of herpesviruses and bacteriophages, implying an evolutionary relationship among the archaeal, bacterial, and eukaryotic viruses.
History
DepositionMar 27, 2022-
Header (metadata) releaseAug 10, 2022-
Map releaseAug 10, 2022-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33148.png

Downloads & links

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Map

FileDownload / File: emd_33148.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.27 Å/pix.
x 400 pix.
= 508. Å		1.27 Å/pix.
x 400 pix.
= 508. Å		1.27 Å/pix.
x 400 pix.
= 508. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.27 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 15.0
Minimum - Maximum-148.383559999999989 - 208.415649999999999
Average (Standard dev.)0.047714412 (±5.514354)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-200-200-200
Dimensions400400400
Spacing400400400
CellA=B=C: 508.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33148_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_33148_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 : Sulfolobus spindle-shaped virus

EntireName: Sulfolobus spindle-shaped virus
Components
  • Virus: Sulfolobus spindle-shaped virus
    • Protein or peptide: VP1
    • Protein or peptide: C131
    • Protein or peptide: B210
    • Protein or peptide: VP4

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Supramolecule #1: Sulfolobus spindle-shaped virus

SupramoleculeName: Sulfolobus spindle-shaped virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2491899 / Sci species name: Sulfolobus spindle-shaped virus / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No

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Macromolecule #1: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus spindle-shaped virus
Molecular weightTheoretical: 9.282206 KDa
SequenceString:
MRWQIRKLRR AEGFNVGLLI GLFIFILVGI VLLPVITSEV SSLTSGTSPA VTGTNATLLN LVPLFYILIL VIVPAVLAYK MYRE

UniProtKB: VP1

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Macromolecule #2: C131

MacromoleculeName: C131 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus spindle-shaped virus
Molecular weightTheoretical: 14.753507 KDa
SequenceString:
MGTKIIINVI FFDIILALLM MSFASIQPPS IANPPTVAQA QAQANITWNL TVGSINWEWL WPVFYFVDWL IWIVTTIFAV VAFIFNVFT TSLSLLASVP IVGPFLLMFA VIINFVLIWE VVKLIRGYDN PG

UniProtKB: Uncharacterized protein

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Macromolecule #3: B210

MacromoleculeName: B210 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus spindle-shaped virus
Molecular weightTheoretical: 23.195996 KDa
SequenceString: MKWPLLLFTV LLIIGFTLIA RAGTISLLST PPVNPPAYSY FYIEFQFLPT NNTPQPYAIF VGPNPNNLTE VAEGYTLSNG TGYARVPVI NAQTEYVDIV WVNQNYTMFE IFPQIQNATT TVTLSANNNQ GFSFSLPTWV SWVIGAVLML IFMGVGWKFM G PAGLAIFG ...String:
MKWPLLLFTV LLIIGFTLIA RAGTISLLST PPVNPPAYSY FYIEFQFLPT NNTPQPYAIF VGPNPNNLTE VAEGYTLSNG TGYARVPVI NAQTEYVDIV WVNQNYTMFE IFPQIQNATT TVTLSANNNQ GFSFSLPTWV SWVIGAVLML IFMGVGWKFM G PAGLAIFG IFGLFIAMFF GLLPSYLMYV ILFIVAIVGA RILTKQLGGG EE

UniProtKB: Uncharacterized protein

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Macromolecule #4: VP4

MacromoleculeName: VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus spindle-shaped virus
Molecular weightTheoretical: 137.071953 KDa
SequenceString: MKRVFLLYII GILLTLFLPL IQTQSAVSLP PLYVEDAVNA EIQQLWSKSP TGVYAFHEAP SVNNSFWPDD NAKFLESIAP WWQSYSSYV NSTLQFLQQS DVNGLFIKRF EYPLNPLQSI TIGNLSGYTN GFYDIVGNPL LNSMRIATYY NPTLAVTYLF G NVVQYPNG ...String:
MKRVFLLYII GILLTLFLPL IQTQSAVSLP PLYVEDAVNA EIQQLWSKSP TGVYAFHEAP SVNNSFWPDD NAKFLESIAP WWQSYSSYV NSTLQFLQQS DVNGLFIKRF EYPLNPLQSI TIGNLSGYTN GFYDIVGNPL LNSMRIATYY NPTLAVTYLF G NVVQYPNG ILVNIEQGLE NPITDGGFGG TGGQNPPWES LNSSSLVNDS IVSIVNNAKT YLNLTGPTFF GTPSEELQYN FP IVNVLPH YLAFQNVNGI LGQYNYQGKF IPFNVTLVLQ SSSINRIYLE FIWENSTSGT YVLTDIPVYF TANGQWQQVV VTV PASAWP KYWNLGALSA VPLLIGIGLD LPGSSPSQTG PTGVYVGDIA TNYPTTFGPQ FNVTNKGSYV VFNESWKSDS LGAT FWIAY VLGQGNAIEV LASAPVNQSW IYVGYNGLAT IGTGYTILET PSGILKNYQN SGNISWTYLG PNFGKWMLLS TNYAP NWIG DFQMLFIFPM AGTSNPYMDT LNNAVYMGDP TEVRNTLYFG NYTTLPGYFQ WVQIAYQNDG NTSGVFGFFL IPSVDY LVN PSVIVNDMFP SSLTAYSPSS IPNYWWEAVW GENYYEGEII YALALLGKYG NSQALQMAQQ AWLSYYNQLK AYNGATY TS SLARFIMATI LLYNITGNTQ YSNAYTQLAN WLLQYQNQSK YAYVYIPMWY HKDVDVPSVN GFATYGYIIN RTAQMDVG T VISGTSIGLN FFEDIPLNTS YGIYLLTNGT GKLPFTYQNV LNVSGTFITY LYMNGGGTAT TANITITVQI AYNGNVLQT IGTAAVDNVP IQPGGISGSP PFYPVKIVVP VLTTVNAPPG STLIIGWNIK APQTVYVLID STNGPSNVTI PLSWPNPFYG LFTIPKIYN PNPGVHNYPQ PYFLDISAMA GQAMMALYAV TKNITYLLDA QLVMNAIHYG PVPMPTYGIL GVPNPPVEPR L WVYANYST VDADYYTYKS ELVSEFGDAI GNNTLASLAI SRVWQRTSYT YPTSYIYYVA RYGSGLQMNS ETQPWGDVAT QF YVNTWSP SNLDLFWASL PNNNYITNQT WNGTALFIHL YAYQQSQVQL IFLTTTVNFN VLVNGNYTNY EANHQIMQIA PTL EPGPNT IIIIPNPKNQ VSQNTNISTT TTTSPLSNAI SGLGITLTQN ELMLLGFVIY FVIIMVTYGV SRNKTITVLS SIVA VAIVY ALALWPTYMA FILGAVGFFM LFYSISRREE E

UniProtKB: VP4

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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: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 49361
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING

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