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- EMDB-51883: Tail fibre of Haloferax tailed virus 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-51883
TitleTail fibre of Haloferax tailed virus 1
Map data
Sample
  • Virus: Haloferax tailed virus 1
    • Protein or peptide: Tail fiber protein of Haloferax tailed virus 1 gp42
    • Protein or peptide: Baseplate hub
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
KeywordsArchaeal virus / tail / VIRUS
Function / homologyBaseplate hub / Uncharacterized protein
Function and homology information
Biological speciesHaloferax tailed virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsZhang D / Daum B / Isupov MN / McLaren M
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: Sci Adv / Year: 2025
Title: Cryo-EM resolves the structure of the archaeal dsDNA virus HFTV1 from head to tail.
Authors: Daniel X Zhang / Michail N Isupov / Rebecca M Davies / Sabine Schwarzer / Mathew McLaren / William S Stuart / Vicki A M Gold / Hanna M Oksanen / Tessa E F Quax / Bertram Daum /
Abstract: While archaeal viruses show a stunning diversity of morphologies, many bear a notable resemblance to tailed bacterial phages. This raises fundamental questions: Do all tailed viruses share a common ...While archaeal viruses show a stunning diversity of morphologies, many bear a notable resemblance to tailed bacterial phages. This raises fundamental questions: Do all tailed viruses share a common origin and do they infect their hosts in similar ways? Answering these questions requires high-resolution structural insights, yet no complete atomic models of archaeal viruses have been available. Here, we present the near-atomic resolution structure of Haloferax tailed virus 1 (HFTV1), an archaeal virus thriving in extreme salinity. Using cryo-electron microscopy, we resolve the architecture and assembly of all structural proteins and capture conformational transitions associated with DNA ejection. Our data reveal genome spooling within the capsid and identify putative receptor-binding and catalytic sites for host recognition and infection. These findings uncover key mechanisms of archaeal virus assembly, principles of virus-host interactions, and evolutionary links connecting archaeal, bacterial, and eukaryotic viruses.
History
DepositionOct 22, 2024-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51883.png

Downloads & links

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Map

FileDownload / File: emd_51883.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 320 pix.
= 432. Å		1.35 Å/pix.
x 320 pix.
= 432. Å		1.35 Å/pix.
x 320 pix.
= 432. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0021
Minimum - Maximum-0.021141276 - 0.044799544
Average (Standard dev.)0.00004802305 (±0.00070730917)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 432.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_51883_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51883_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Haloferax tailed virus 1

EntireName: Haloferax tailed virus 1
Components
  • Virus: Haloferax tailed virus 1
    • Protein or peptide: Tail fiber protein of Haloferax tailed virus 1 gp42
    • Protein or peptide: Baseplate hub
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: Haloferax tailed virus 1

SupramoleculeName: Haloferax tailed virus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / NCBI-ID: 2507575 / Sci species name: Haloferax tailed virus 1 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Haloferax gibbonsii (archaea)

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Macromolecule #1: Tail fiber protein of Haloferax tailed virus 1 gp42

MacromoleculeName: Tail fiber protein of Haloferax tailed virus 1 gp42 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Haloferax tailed virus 1
Molecular weightTheoretical: 45.959707 KDa
SequenceString: MADTTIIDAV VFPQDDGTGV SNGDEDYDSA GYLASLARYA GDGSYVGGDS TGSPTLQFAN IDTANEEVDI QPGHAFILES GHIVQSGSQ KTYDTNLPDS VPYVVILPSS VTNVPLDTDV DNDVWLAVDP TSNDSVYIRS GNGLSAPSDP SVKLGTVNSS T GSTTRPND ...String:
MADTTIIDAV VFPQDDGTGV SNGDEDYDSA GYLASLARYA GDGSYVGGDS TGSPTLQFAN IDTANEEVDI QPGHAFILES GHIVQSGSQ KTYDTNLPDS VPYVVILPSS VTNVPLDTDV DNDVWLAVDP TSNDSVYIRS GNGLSAPSDP SVKLGTVNSS T GSTTRPND LADHSVDALN ATTIDASDTV TGDTVDATTT LTDAAGVSHT GELEDINHGS KHEDGGSDEI SVGGLSGDLA DP QDPKAHA ASHSADSADE ISVENLSTTG SADTVPISQG DGTLSMGSIV PTDLQWREDS NSPQTDTNVG TSTYTIADTF DEY LIRVQV FEESSAPGTV ELRAEGNSQS SYDYISEDGT TTSAATSIPC IELQADSSTI SVFGASGRFS GQWEFRSQPN TSTN LATAG FLAVISSPLG SLELFRAANN FSVTWEVFGR DIGPAGVP

UniProtKB: Uncharacterized protein

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Macromolecule #2: Baseplate hub

MacromoleculeName: Baseplate hub / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloferax tailed virus 1
Molecular weightTheoretical: 102.541312 KDa
SequenceString: MPQLGDSKLG ESQLGSPGTL KQGVEWTVVV DGEEQNNVWD VQVVDTANPF GDYAVFKMDD RGGQAFEAYP RGTRVEAYVS EGTEPLDNR FTGYVVERRE NEQQGADVLE VEAYSFDQFL RRNTVTNDQT GNTISQALAD IIQTDTPVRF NAANITVGDD Q ELTRSYQG ...String:
MPQLGDSKLG ESQLGSPGTL KQGVEWTVVV DGEEQNNVWD VQVVDTANPF GDYAVFKMDD RGGQAFEAYP RGTRVEAYVS EGTEPLDNR FTGYVVERRE NEQQGADVLE VEAYSFDQFL RRNTVTNDQT GNTISQALAD IIQTDTPVRF NAANITVGDD Q ELTRSYQG DPVENALRDF AFKSTNEDFG VGDDLEFFFQ PRETVHIDRG VDNTQWFRYD IPELGKEAIN EVEVWFDDGE ES VIVDDGT DKLDLQDSLG LPSPGTQRKE LQRPLVTDIS DAEDIGRKYL AFRNSTLSGT VTTYGLYDAE PGDTIDITID PRG IDEEFV IAAIEYRWGV DETILTVVEK RGDVDDILSE LSESVQRIEM QGANRDAPKN RITTTNAAAI VSVDVDAGGT SADA DRFVN DGRNAVRDAW TGAGNPDIAN IVVGDDNSGL SRTNTTLGNQ TDSVSVTESL PSAKVVEYSA TLTQSGVEEI GLETS TGTL LTRATFETPV DLSSDTVTVT LTVSNDDSVS RGVMTNDGQT AVRDVLADNS PTLPTDYGYG DDSTAVAETD TTLGNE LAN TSLEEILIQS ASSVSAWNTI LGTLASTYPL VVSSSGIRPA QTAWTTESDN LAQSGTALVT VGDYSNGEAE GLDSPGD TL ELSFTPEHDI PGEEFALWCR IETDLGGTDP GPEITVTLDI DGDTYSWVPI GTNTALGLNW YDLANNTFGG SSTYPDTD I PEGSTVTLSI EATSSSVSGQ GHAVDVMAPL DALTRVTGGS DATSAYTFDN NNGGSGGYLD GPELYPDQLI LSLETATTR RNVSEARFTL TANDTSGNFY VELANDGSTF NRVNNATSGS VTFASPDTNV DTNISLNRYG SRSTATPQTG FNAQEIDNWE LYADIDAVL PDDIGVTLSR AIIPPNTSGI VGQTVREAGL KSGSTLLTRH ILAEFLLDTD QRLASSESTR FTSDN

UniProtKB: Baseplate hub

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 9 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

MicroscopeTFS KRIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: TFS FALCON 4i (4k x 4k) / #0 - Average electron dose: 50.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 (6k x 4k) / #1 - Average electron dose: 54.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID2
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 336454
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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