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- EMDB-18559: C1 turret to capsid interface of full Haloferax tailed virus 1 ad... -

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Basic information

Entry
Database: EMDB / ID: EMD-18559
TitleC1 turret to capsid interface of full Haloferax tailed virus 1 adjacent to the portal-capsid interface.
Map data
Sample
  • Virus: Haloferax tailed virus 1
    • Protein or peptide: Prokaryotic polysaccharide deacetylase
    • Protein or peptide: gp30
    • Protein or peptide: HK97 gp5-like major capsid protein
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
KeywordsArchaeal virus / turret / turret capsid interface / Mg ions / VIRUS
Function / homologyNodB homology domain / Polysaccharide deacetylase / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / Glycoside hydrolase/deacetylase, beta/alpha-barrel / carbohydrate metabolic process / HK97 gp5-like major capsid protein / Prokaryotic polysaccharide deacetylase
Function and homology information
Biological speciesHaloferax tailed virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 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 2, 2023-
Header (metadata) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18559.png

Downloads & links

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Map

FileDownload / File: emd_18559.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.17 Å/pix.
x 256 pix.
= 299.776 Å		1.17 Å/pix.
x 256 pix.
= 299.776 Å		1.17 Å/pix.
x 256 pix.
= 299.776 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.171 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.024
Minimum - Maximum-0.038767755 - 0.08683626
Average (Standard dev.)-0.00008577035 (±0.0073124543)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 299.776 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_18559_additional_1.map
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Half map: #1

Fileemd_18559_half_map_1.map
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Half map: #2

Fileemd_18559_half_map_2.map
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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: Prokaryotic polysaccharide deacetylase
    • Protein or peptide: gp30
    • Protein or peptide: HK97 gp5-like major capsid protein
  • Ligand: ZINC ION
  • 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-#3 / 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: Prokaryotic polysaccharide deacetylase

MacromoleculeName: Prokaryotic polysaccharide deacetylase / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Haloferax tailed virus 1
Molecular weightTheoretical: 45.242082 KDa
SequenceString: MTGLNPDGLG RTAAFSNTSA ESVSAVDATI DRLYAQDRIE IPTDSRQLFS TRGTVLRNFE DLSGWTANIG SLSAETSDVY VGSQSARLT ASSSAVDIRY SFGTAQDFTG KGFSMALKRI DVSGSSDSTP IKIRLVDGNT NYRTFSARCR PGGGDEWGRR D FGFESEDT ...String:
MTGLNPDGLG RTAAFSNTSA ESVSAVDATI DRLYAQDRIE IPTDSRQLFS TRGTVLRNFE DLSGWTANIG SLSAETSDVY VGSQSARLT ASSSAVDIRY SFGTAQDFTG KGFSMALKRI DVSGSSDSTP IKIRLVDGNT NYRTFSARCR PGGGDEWGRR D FGFESEDT GFDVTNVQTM TVTTNSRSSI DILVDDIRVV DSSGTGQVIV TIDDVHTGDK TAAEVFGRYG IPIGLAANAK FL DQSSSKL TTQEFKDLLA KPHVYAVNHG YNHYDYGSYS IDEIEDDVIR GKYELQDLGV REPNINHYVY PSGNYAQESI DML SNYHVM SWGTGAESFD ALTPNQLTSP WHNLRCSFDS GTAEAEQAVN DAATYNQTAH IYFHSDNVTQ SEMESVAQTI NSAD VTPIT LMDFYNQQ

UniProtKB: Prokaryotic polysaccharide deacetylase

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Macromolecule #2: gp30

MacromoleculeName: gp30 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Haloferax tailed virus 1
Molecular weightTheoretical: 12.005731 KDa
SequenceString:
MTDTIVNVQG SFFSASASGV ADTESLLIDP QDAKFGAIEI HNIA(NEP)GGSVD VELLTSSDDT ELVEDAAVTL DSFTGE GIS QGNQIEASDN TNTYIRITNT SGGAIDIIAT GREVSQ

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Macromolecule #3: HK97 gp5-like major capsid protein

MacromoleculeName: HK97 gp5-like major capsid protein / type: protein_or_peptide / ID: 3 / Number of copies: 6 / 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 #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 50 / 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 recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / 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

CTF correctionSoftware - Name: RELION (ver. 4.0-beta) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 102012
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Initial model type: in silico model
RefinementSpace: RECIPROCAL / Protocol: AB INITIO MODEL
Output model

PDB-8qpq:
C1 turret to capsid interface of full Haloferax tailed virus 1 adjacent to the portal-capsid interface.

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