9H7V | pdb_00009h7v

The baseplate assembly of Haloferax tailed virus 1.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9H7V

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 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.

Macromolecule Content 

  • Total Structure Weight: 981.29 kDa 
  • Atom Count: 54,689 
  • Modeled Residue Count: 7,347 
  • Deposited Residue Count: 9,276 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tail tube protein158Haloferax tailed virus 1Mutation(s): 0 
UniProt
Find proteins for A0A410N6U0 (Haloferax tailed virus 1)
Explore A0A410N6U0 
Go to UniProtKB:  A0A410N6U0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A410N6U0
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Baseplate to tube adapter protein gp41G [auth BA],
H [auth BB],
I [auth BC]
285Haloferax tailed virus 1Mutation(s): 0 
UniProt
Find proteins for A0A410N6X8 (Haloferax tailed virus 1)
Explore A0A410N6X8 
Go to UniProtKB:  A0A410N6X8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A410N6X8
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Baseplate hubJ [auth BD],
K [auth BE],
L [auth BF]
954Haloferax tailed virus 1Mutation(s): 0 
UniProt
Find proteins for A0A410N6T6 (Haloferax tailed virus 1)
Explore A0A410N6T6 
Go to UniProtKB:  A0A410N6T6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A410N6T6
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Tail fiber protein gp42285Haloferax tailed virus 1Mutation(s): 0 
UniProt
Find proteins for A0A410N721 (Haloferax tailed virus 1)
Explore A0A410N721 
Go to UniProtKB:  A0A410N721
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A410N721
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Phate tail tape measure protein341Haloferax tailed virus 1Mutation(s): 0 
UniProt
Find proteins for A0A410N6W4 (Haloferax tailed virus 1)
Explore A0A410N6W4 
Go to UniProtKB:  A0A410N6W4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A410N6W4
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
(Subject of Investigation/LOI)

Query on ZN



Download:Ideal Coordinates CCD File
DC [auth BM]
GB [auth BG]
HC [auth BN]
KB [auth BH]
RB [auth BJ]
DC [auth BM],
GB [auth BG],
HC [auth BN],
KB [auth BH],
RB [auth BJ],
VB [auth BK]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
(Subject of Investigation/LOI)

Query on K



Download:Ideal Coordinates CCD File
CB [auth BF]
IA [auth BD]
JA [auth BD]
KA [auth BD]
LA [auth BE]
CB [auth BF],
IA [auth BD],
JA [auth BD],
KA [auth BD],
LA [auth BE],
UA [auth BE],
VA [auth BE],
WA [auth BE]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
AB [auth BF]
AC [auth BM]
BA [auth BD]
BB [auth BF]
BC [auth BM]
AB [auth BF],
AC [auth BM],
BA [auth BD],
BB [auth BF],
BC [auth BM],
CA [auth BD],
CC [auth BM],
DA [auth BD],
DB [auth BG],
EA [auth BD],
EB [auth BG],
EC [auth BN],
FA [auth BD],
FB [auth BG],
FC [auth BN],
GA [auth BD],
GC [auth BN],
HA [auth BD],
HB [auth BH],
IB [auth BH],
IC [auth BO],
JB [auth BH],
JC [auth BO],
KC [auth BO],
LB [auth BI],
MA [auth BE],
MB [auth BI],
NA [auth BE],
NB [auth BI],
OA [auth BE],
OB [auth BJ],
PA [auth BE],
PB [auth BJ],
QA [auth BE],
QB [auth BJ],
RA [auth BE],
SA [auth BE],
SB [auth BK],
TA [auth BE],
TB [auth BK],
UB [auth BK],
WB [auth BL],
XA [auth BF],
XB [auth BL],
YA [auth BF],
YB [auth BL],
ZA [auth BF],
ZB [auth BL]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC5

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