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- EMDB-51866: Tail of full Haloferax tailed virus 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-51866
TitleTail of full Haloferax tailed virus 1
Map data
Sample
  • Virus: Haloferax tailed virus 1
    • Protein or peptide: Baseplate hub
    • Protein or peptide: Phate tail tape measure protein
    • Protein or peptide: Baseplate to tube adapter protein gp41
    • Protein or peptide: Tail tube protein
    • Protein or peptide: SPP1 gp17-like tail completion protein
    • Protein or peptide: HK97 gp6-like/SPP1 gp15-like head-tail connector
    • Protein or peptide: Portal protein
  • Ligand: MAGNESIUM ION
KeywordsArchaeal virus / portal / tail / baseplate / tape measure protein / VIRUS
Function / homologyPortal protein / HK97 gp6-like/SPP1 gp15-like head-tail connector / Baseplate hub / Tail tube protein / SPP1 gp17-like tail completion protein / Phate tail tape measure protein / Uncharacterized protein
Function and homology information
Biological speciesHaloferax tailed virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 2.44 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 21, 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_51866.png

Downloads & links

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Map

FileDownload / File: emd_51866.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.17 Å/pix.
x 768 pix.
= 899.328 Å		1.17 Å/pix.
x 768 pix.
= 899.328 Å		1.17 Å/pix.
x 768 pix.
= 899.328 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.171 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.0253447 - 0.07305847
Average (Standard dev.)0.00027756437 (±0.0018455108)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions768768768
Spacing768768768
CellA=B=C: 899.328 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_51866_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51866_half_map_2.map
Projections & Slices
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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: Baseplate hub
    • Protein or peptide: Phate tail tape measure protein
    • Protein or peptide: Baseplate to tube adapter protein gp41
    • Protein or peptide: Tail tube protein
    • Protein or peptide: SPP1 gp17-like tail completion protein
    • Protein or peptide: HK97 gp6-like/SPP1 gp15-like head-tail connector
    • Protein or peptide: Portal protein
  • Ligand: MAGNESIUM 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-#7 / NCBI-ID: 2507575 / Sci species name: Haloferax tailed virus 1 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Haloferax gibbonsii (archaea)

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Macromolecule #1: Baseplate hub

MacromoleculeName: Baseplate hub / type: protein_or_peptide / ID: 1 / Number of copies: 3 / 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 #2: Phate tail tape measure protein

MacromoleculeName: Phate tail tape measure protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Haloferax tailed virus 1
Molecular weightTheoretical: 36.043656 KDa
SequenceString: MVAIRSEGVS ETQQNLEGVE NAMEDTADSA GDSAAELETF SKRFKGAMGA AVSALAIGTA GLLSQVPVVG EAMGGLGAII DALTMKIDE DARPAVGSFT DDLYEVAEAT YEADSSLEAF QTALDGVNTA IDDVAVSTLQ TEIEELTGIT IPKNWLDFGW D IMTLDARQ ...String:
MVAIRSEGVS ETQQNLEGVE NAMEDTADSA GDSAAELETF SKRFKGAMGA AVSALAIGTA GLLSQVPVVG EAMGGLGAII DALTMKIDE DARPAVGSFT DDLYEVAEAT YEADSSLEAF QTALDGVNTA IDDVAVSTLQ TEIEELTGIT IPKNWLDFGW D IMTLDARQ TMDNIETIIN EFPEDFGTML KSIDPRAKKG WDILTKSADM FINDLTSRID SGVNDVRGFF TGLASDLNEW GG NVASDAR EWGTNLIDKF TGGIRSKISG LRNWLSELRN IGAEVGIDVP TIGGGGDGGG GGGNSSRQPF AGGFFGGGNA TID GRQISE STGRYRSDPS RRRGI

UniProtKB: Phate tail tape measure protein

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Macromolecule #3: Baseplate to tube adapter protein gp41

MacromoleculeName: Baseplate to tube adapter protein gp41 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Haloferax tailed virus 1
Molecular weightTheoretical: 30.425914 KDa
SequenceString: MVDATLSRGG TSVDIPLVEE GGEILLSSTF GKPEVNVRKS GGSLNPRVID SWSGLQTFQL VGKLYDYSTS HQLADLVKTA STTPLELQI PQDAYPDTVT VAPAAGQASA LTLEYPAGRK DLVDVSLSLT RVDPNSVRGV GDQQATTPTT TGTGPVEVTA G GTTVQLPS ...String:
MVDATLSRGG TSVDIPLVEE GGEILLSSTF GKPEVNVRKS GGSLNPRVID SWSGLQTFQL VGKLYDYSTS HQLADLVKTA STTPLELQI PQDAYPDTVT VAPAAGQASA LTLEYPAGRK DLVDVSLSLT RVDPNSVRGV GDQQATTPTT TGTGPVEVTA G GTTVQLPS SGLSVERTVG RPNDAVRRVP RQADPRYEVK AKVTNDVFTF SFETLDNIPA TLNALTDNVF REQLGRDGVT LD FNGLLGL GSVKAIPVGS SPFRQVHQAG RGWVTVPTLE FRRIYSNE

UniProtKB: Uncharacterized protein

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Macromolecule #4: Tail tube protein

MacromoleculeName: Tail tube protein / type: protein_or_peptide / ID: 4 / Number of copies: 66 / Enantiomer: LEVO
Source (natural)Organism: Haloferax tailed virus 1
Molecular weightTheoretical: 17.177463 KDa
SequenceString:
MATSPEGIWS NSGALTFEDP ADDSEILFAG VRDVTITPAY EHAELYTIDS TFRDEVKRYE HNVNVEITYA KFSLEFAQEW LGGPGATAT ASQDDSDPMK FNLENVTPSA SGGFERTTAV ENVVFPELPL DSATYGEYEE YSLTGSGRSV TNLADTSGV

UniProtKB: Tail tube protein

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Macromolecule #5: SPP1 gp17-like tail completion protein

MacromoleculeName: SPP1 gp17-like tail completion protein / type: protein_or_peptide / ID: 5 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Haloferax tailed virus 1
Molecular weightTheoretical: 17.458789 KDa
SequenceString:
MATTSASHHV QAIIDLLEAA PDADWTPTQT PTVKRYWDDA QSERGPGADM PAILYVWSPT TSSLDRFSMD GDVFDQNDSI EVQAWSFDE TEVEQLQGDI VQILSEYLDD NEVQTPYSDV APTGTNDFRE QTPARTTGHY IMSVEVETRG LSETAKNA

UniProtKB: SPP1 gp17-like tail completion protein

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Macromolecule #6: HK97 gp6-like/SPP1 gp15-like head-tail connector

MacromoleculeName: HK97 gp6-like/SPP1 gp15-like head-tail connector / type: protein_or_peptide / ID: 6 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Haloferax tailed virus 1
Molecular weightTheoretical: 15.585868 KDa
SequenceString:
MPDPSIDEVS KSDWDALTTQ EQDDIISQVE NLSSTGWVNT SRERKAEAIR SAIAERDTLY SGNMSRLPTL DGDAEYFTLY LSAHKIQLF EGGEAQSESG EGGSVSYSTG GGGEKDLQKT RYGRMALEYV WEDNSIAALR TY

UniProtKB: HK97 gp6-like/SPP1 gp15-like head-tail connector

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Macromolecule #7: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 7 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Haloferax tailed virus 1
Molecular weightTheoretical: 75.680906 KDa
SequenceString: MPKYNLRIGN RRVPIASTDT PLSEAIGKRL ASSTPQTNVD SMGGGHSYQF NGQDLTFEDL RDIKDVRDSG GQVAQLMDYK ALLNFGEGC EIHVEGDDET KQLVDGEPMT LSEWLEDAFP HLDLLVLDLG GDALWYPYAV GEIQETITGE FKEALPAEPW T LMPESDAQ ...String:
MPKYNLRIGN RRVPIASTDT PLSEAIGKRL ASSTPQTNVD SMGGGHSYQF NGQDLTFEDL RDIKDVRDSG GQVAQLMDYK ALLNFGEGC EIHVEGDDET KQLVDGEPMT LSEWLEDAFP HLDLLVLDLG GDALWYPYAV GEIQETITGE FKEALPAEPW T LMPESDAQ GKVQAWHQRT KTHGGYQTQT LPADDLW(HIP)IV INKASARDEV GISEVLRNKD EIQAFKQNEA AINQAIEL H GFPQR(HIP)VKVG KEDGAPVRDN DLRRVRTIFD PRTTDANTAY FTGQDVDVET LEA(HIP)NFDYSA IHEMDMRNLT T ALGLPLEA GNVGADGLGS GKPAELRFAL LKLAIKANQR SFSVQFVERV MRPVVRDYSP FDHEADIRLE INDPLEDIGE VA DLIQQVG DYMTNEQVAE KLDLPAPEDD EVADSYRSPA DMEKDEAGVQ DEPFGGMFAG RDMGNRCLGE GITDDELQHA PEW DRPLLE MYQGVTNPES DTSRTLVSFS SSGTPEFVLE RIRESIMDGA LFSEFDNIPS SRLMELRQTF ADELGTDNFT LDSI TDALM DFEADLTRDA AERIARTESS AVLNHAREIS YEERGEGNEL FYWTGADLGD SRQTEACAWL IRQTNPFSGG TPVPM NELR DMVDEAPSHD DSMDNNLARP DSWVVHPNER SSFVKAPPNW EQL

UniProtKB: Portal protein

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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 15 / Formula: MG
Molecular weightTheoretical: 24.305 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: 2.44 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 116880
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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