9GS0 | pdb_00009gs0

Capsid of full Haloferax tailed virus 1 without turret head protein gp31.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.37 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HK97 gp5-like major capsid protein396Haloferax tailed virus 1Mutation(s): 0 
UniProt
Find proteins for A0A410N6T9 (Haloferax tailed virus 1)
Explore A0A410N6T9 
Go to UniProtKB:  A0A410N6T9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A410N6T9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid stabilization protein137Haloferax tailed virus 1Mutation(s): 0 
UniProt
Find proteins for A0A410N6Q7 (Haloferax tailed virus 1)
Explore A0A410N6Q7 
Go to UniProtKB:  A0A410N6Q7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A410N6Q7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Gp30115Haloferax tailed virus 1Mutation(s): 0 
UniProt
Find proteins for A0A410N6V5 (Haloferax tailed virus 1)
Explore A0A410N6V5 
Go to UniProtKB:  A0A410N6V5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A410N6V5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
K (Subject of Investigation/LOI)
Query on K

Download Ideal Coordinates CCD File 
EB [auth AI],
FB [auth AL],
GB [auth AO]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
AA [auth AB]
AB [auth AF]
BA [auth AB]
BB [auth AF]
CA [auth AB]
AA [auth AB],
AB [auth AF],
BA [auth AB],
BB [auth AF],
CA [auth AB],
CB [auth AF],
DA [auth AB],
DB [auth AF],
EA [auth AB],
FA [auth AB],
GA [auth AB],
HA [auth AB],
HB [auth As],
IA [auth AC],
IB [auth At],
JA [auth AC],
JB [auth Au],
KA [auth AC],
KB [auth Av],
LA [auth AC],
LB [auth Aw],
MA [auth AC],
MB [auth Ax],
NA [auth AC],
NB [auth AG],
OA [auth AD],
OB [auth AG],
PA [auth AD],
PB [auth AG],
QA [auth AD],
QB [auth AG],
RA [auth AD],
RB [auth AG],
SA [auth AD],
SB [auth AG],
TA [auth AD],
U [auth AA],
UA [auth AE],
V [auth AA],
VA [auth AE],
W [auth AA],
WA [auth AE],
X [auth AA],
XA [auth AE],
Y [auth AA],
YA [auth AE],
Z [auth AA],
ZA [auth AE]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.37 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC5.8.0267
MODEL REFINEMENTUCSF ChimeraX
MODEL REFINEMENTISOLDE

Structure Validation

View Full Validation Report



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