9H4P | pdb_00009h4p

Tail of full Haloferax tailed virus 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.44 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM resolves the structure of the archaeal dsDNA virus HFTV1 from head to tail.

Zhang, D.X.Isupov, M.N.Davies, R.M.Schwarzer, S.McLaren, M.Stuart, W.S.Gold, V.A.M.Oksanen, H.M.Quax, T.E.F.Daum, B.

(2025) Sci Adv 11: eadx1178-eadx1178

  • DOI: https://doi.org/10.1126/sciadv.adx1178
  • Primary Citation of Related Structures:  
    8QPG, 8QPQ, 8QQN, 8QSI, 8QSY, 9FKB, 9GS0, 9H4P, 9H5B, 9H7V

  • PubMed 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 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.


  • Organizational Affiliation
    • Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Baseplate hubA [auth BD],
B [auth BE],
C [auth BF]
954Haloferax tailed virus 1Mutation(s): 0 
UniProt
Find proteins for A0A410N6T6 (Haloferax tailed virus 1)
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Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A410N6T6
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phate tail tape measure protein341Haloferax tailed virus 1Mutation(s): 0 
UniProt
Find proteins for A0A410N6W4 (Haloferax tailed virus 1)
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UniProt GroupA0A410N6W4
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Baseplate to tube adapter protein gp41J [auth BA],
K [auth BB],
L [auth BC]
285Haloferax tailed virus 1Mutation(s): 0 
UniProt
Find proteins for A0A410N6X8 (Haloferax tailed virus 1)
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UniProt GroupA0A410N6X8
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Tail tube protein158Haloferax tailed virus 1Mutation(s): 0 
UniProt
Find proteins for A0A410N6U0 (Haloferax tailed virus 1)
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UniProt GroupA0A410N6U0
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
SPP1 gp17-like tail completion protein157Haloferax tailed virus 1Mutation(s): 0 
UniProt
Find proteins for A0A410N6U9 (Haloferax tailed virus 1)
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UniProt GroupA0A410N6U9
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
HK97 gp6-like/SPP1 gp15-like head-tail connector141Haloferax tailed virus 1Mutation(s): 0 
UniProt
Find proteins for A0A410N6S3 (Haloferax tailed virus 1)
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UniProt GroupA0A410N6S3
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Portal protein675Haloferax tailed virus 1Mutation(s): 0 
UniProt
Find proteins for A0A410N6Q2 (Haloferax tailed virus 1)
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UniProt GroupA0A410N6Q2
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
ED [auth BD]
FD [auth BE]
GD [auth BF]
HD [auth PT]
ID [auth PM]
ED [auth BD],
FD [auth BE],
GD [auth BF],
HD [auth PT],
ID [auth PM],
JD [auth PN],
KD [auth PO],
LD [auth PP],
MD [auth PQ],
ND [auth PR],
OD [auth PS],
PD [auth PU],
QD [auth PU],
RD [auth PV],
SD [auth PW]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
HIP
Query on HIP
AD [auth PI]
BD [auth PJ]
CD [auth PK]
DD [auth PL]
SC [auth PA]
AD [auth PI],
BD [auth PJ],
CD [auth PK],
DD [auth PL],
SC [auth PA],
TC [auth PB],
UC [auth PC],
VC [auth PD],
WC [auth PE],
XC [auth PF],
YC [auth PG],
ZC [auth PH]
L-PEPTIDE LINKINGC6 H11 N3 O5 PHIS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.44 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC5.8.0267

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union--

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-27
    Type: Initial release
  • Version 1.1: 2025-10-22
    Changes: Data collection, Database references