[English] 日本語
Yorodumi
- EMDB-33148: Tail structure of bacteriophage SSV19 -

+
Open data


ID or keywords:

Loading...

-
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
Function / homology
Function and homology information


membrane => GO:0016020 / carbohydrate metabolic process / structural molecule activity
Similarity search - Function
Structural protein VP1/VP3 / Structural protein VP1/VP3 / 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-
UpdateAug 10, 2022-
Current statusAug 10, 2022Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_33148.png

Downloads & links

-
Map

FileDownload / File: emd_33148.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.27 Å
Density
Contour LevelBy AUTHOR: 15.0
Minimum - Maximum-148.38356 - 208.41565
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 °

-
Supplemental data

-
Half map: #2

Fileemd_33148_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_33148_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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

-
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

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

-
Electron microscopy

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

-
Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 49361

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more