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- EMDB-51530: Capsid of full Haloferax tailed virus 1 without turret head prote... -

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Basic information

Entry
Database: EMDB / ID: EMD-51530
TitleCapsid of full Haloferax tailed virus 1 without turret head protein gp31.
Map data
Sample
  • Virus: Haloferax tailed virus 1
    • Protein or peptide: HK97 gp5-like major capsid protein
    • Protein or peptide: Capsid stabilization protein
    • Protein or peptide: Gp30
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM ION
KeywordsArchaeal virus / turret / capsid / VIRUS
Function / homologyCapsid stabilization protein / HK97 gp5-like major capsid protein / Gp30
Function and homology information
Biological speciesHaloferax tailed virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 2.37 Å
AuthorsZhang D / Daum B / Isupov MN / McLaren M / Stuart W
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
DepositionSep 13, 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_51530.png

Downloads & links

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Map

FileDownload / File: emd_51530.map.gz / Format: CCP4 / Size: 2.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.17 Å/pix.
x 896 pix.
= 1049.216 Å		1.17 Å/pix.
x 896 pix.
= 1049.216 Å		1.17 Å/pix.
x 896 pix.
= 1049.216 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.171 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.19
Minimum - Maximum-1.1294665 - 2.5792527
Average (Standard dev.)0.016027447 (±0.13655081)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions896896896
Spacing896896896
CellA=B=C: 1049.2161 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_51530_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_51530_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: HK97 gp5-like major capsid protein
    • Protein or peptide: Capsid stabilization protein
    • Protein or peptide: Gp30
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM 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-#3 / 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: HK97 gp5-like major capsid protein

MacromoleculeName: HK97 gp5-like major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Haloferax tailed virus 1
Molecular weightTheoretical: 43.544406 KDa
SequenceString: MLMEAALPGS DVSAREVAKV WPGAKKGDYS FLQGNQSRSL EAEMTRTARA EAGTDRHRAL KDYAVDADNL PKTLSAGSKH LTEDGDVIE ARLDDAIPRM LFAASDPEYV DTLFREQLLE VVMEGRELRK VAREASNVIN ANTRVGDVPI ASDEEFARPT G QGAEIRDD ...String:
MLMEAALPGS DVSAREVAKV WPGAKKGDYS FLQGNQSRSL EAEMTRTARA EAGTDRHRAL KDYAVDADNL PKTLSAGSKH LTEDGDVIE ARLDDAIPRM LFAASDPEYV DTLFREQLLE VVMEGRELRK VAREASNVIN ANTRVGDVPI ASDEEFARPT G QGAEIRDD GETYTTVAWN ATKLTEGSRV TDEMRDQAMV DLIERNIQRV GASLENGINR VFLTELVDNA QNNHDTAGSN QG YQALNSA VGEVDKDDFR PDTYVTHPDY RTQLFNDTNL AYANRAGTNE VLRNREDAPI VGDIAGLDMH AAMSSATYDD GTD IGWSGG SETWGFSSDG DKGAVVYDRD NIHTILYAPN GQDVEIKDYE DPIRDITGVN GRLHVDCQYS QGRSSATVQY

UniProtKB: HK97 gp5-like major capsid protein

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Macromolecule #2: Capsid stabilization protein

MacromoleculeName: Capsid stabilization protein / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Haloferax tailed virus 1
Molecular weightTheoretical: 13.888911 KDa
SequenceString:
MATETQGEHT FPVEVLISGE ELRGYTAGEA LSAGEPVYLS GDYEVSASSA DGGEFLGVNL YDVASGEPVA LAGDDCEVRV EVSEQVTAN DEILPDGLGT FETVATSAAS AGVAIVQEGA ASGEVCEAYI FAVQGTTA

UniProtKB: Capsid stabilization protein

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Macromolecule #3: Gp30

MacromoleculeName: Gp30 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Haloferax tailed virus 1
Molecular weightTheoretical: 11.92676 KDa
SequenceString:
MTDTIVNVQG SFFSASASGV ADTESLLIDP QDAKFGAIEI HNIAHGGSVD VELLTSSDDT ELVEDAAVTL DSFTGEGISQ GNQIEASDN TNTYIRITNT SGGAIDIIAT GREVSQ

UniProtKB: Gp30

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 48 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 5 / Number of copies: 3 / Formula: K
Molecular weightTheoretical: 39.098 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 recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.37 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2512500
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: AB INITIO MODEL
Output model

PDB-9gs0:
Capsid of full Haloferax tailed virus 1 without turret head protein gp31.

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