8QPQ | pdb_00008qpq

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 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
Prokaryotic polysaccharide deacetylaseA [auth TC],
H [auth TA],
I [auth TB]
413Haloferax tailed virus 1Mutation(s): 0 
UniProt
Find proteins for A0A410N6W3 (Haloferax tailed virus 1)
Explore A0A410N6W3 
Go to UniProtKB:  A0A410N6W3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A410N6W3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
DA [auth TA],
FA [auth TB],
P [auth TC]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
AA [auth TH]
AB [auth LE]
BA [auth TI]
BB [auth LE]
CA [auth TI]
AA [auth TH],
AB [auth LE],
BA [auth TI],
BB [auth LE],
CA [auth TI],
CB [auth LE],
DB [auth LE],
EA [auth TA],
EB [auth LD],
FB [auth LD],
GA [auth TB],
GB [auth LD],
HA [auth LA],
HB [auth LD],
IA [auth LA],
IB [auth LD],
JA [auth LA],
JB [auth LD],
KA [auth LA],
KB [auth LC],
LA,
LB [auth LC],
MA [auth LA],
MB [auth LC],
NA [auth LA],
NB [auth LC],
OA [auth LB],
OB [auth LC],
PA [auth LB],
PB [auth LC],
Q [auth TC],
QA [auth LB],
R [auth TD],
RA [auth LB],
S [auth TD],
SA [auth LB],
T [auth TE],
TA [auth LB],
U [auth TE],
UA [auth LF],
V [auth TF],
VA [auth LF],
W [auth TF],
WA [auth LF],
X [auth TG],
XA [auth LF],
Y [auth TG],
YA [auth LF],
Z [auth TH],
ZA [auth LE]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
NEP
Query on NEP
B [auth TD]
C [auth TE]
D [auth TF]
E [auth TG]
F [auth TH]
B [auth TD],
C [auth TE],
D [auth TF],
E [auth TG],
F [auth TH],
G [auth TI]
L-PEPTIDE LINKINGC6 H10 N3 O5 PHIS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC

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: 2024-10-09
    Type: Initial release
  • Version 1.1: 2025-10-22
    Changes: Data collection, Database references