8QSY | pdb_00008qsy

Portal capsid interface of full Haloferax tailed virus 1.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.68 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)
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Go to UniProtKB:  A0A410N6T9
Entity Groups  
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UniProt GroupA0A410N6T9
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid stabilization protein137Haloferax tailed virus 1Mutation(s): 0 
UniProt
Find proteins for A0A410N6Q7 (Haloferax tailed virus 1)
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UniProt GroupA0A410N6Q7
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Hypothetical protein gp21TA [auth P5],
UA [auth P6],
VA [auth P7],
WA [auth P8],
XA [auth P9]
82Haloferax tailed virus 1Mutation(s): 0 
UniProt
Find proteins for A0A410N6V4 (Haloferax tailed virus 1)
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UniProt GroupA0A410N6V4
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Entity ID: 4
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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Entity ID: 5
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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  • 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 
AG [auth LK]
DD [auth JI]
FD [auth JJ]
GD [auth JK]
IH [auth MI]
AG [auth LK],
DD [auth JI],
FD [auth JJ],
GD [auth JK],
IH [auth MI],
JH [auth MJ],
KH [auth MJ],
LH [auth MK],
OE [auth KI],
PE [auth KJ],
QE [auth KK],
SI [auth NI],
TI [auth NJ],
UI [auth NK],
VI [auth P6],
XF [auth LI],
ZF [auth LJ]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
AC [auth JA]
AD [auth JF]
AE [auth KD]
AF [auth LB]
AH [auth ME]
AC [auth JA],
AD [auth JF],
AE [auth KD],
AF [auth LB],
AH [auth ME],
AI [auth NC],
AJ [auth PO],
BC [auth JB],
BD [auth JF],
BE [auth KD],
BF [auth LB],
BG [auth MA],
BH [auth ME],
BI [auth NC],
BJ [auth PP],
CC [auth JB],
CD [auth JI],
CE [auth KD],
CF [auth LC],
CG [auth MA],
CH [auth MF],
CI [auth ND],
CJ [auth PP],
DC [auth JB],
DE [auth KE],
DF [auth LC],
DG [auth MA],
DH [auth MF],
DI [auth ND],
DJ [auth PQ],
EC [auth JB],
ED [auth JI],
EE [auth KE],
EF [auth LC],
EG [auth MA],
EH [auth MF],
EI [auth ND],
EJ [auth PQ],
FC [auth JB],
FE [auth KE],
FF [auth LC],
FG [auth MA],
FH [auth MF],
FI [auth ND],
FJ [auth PR],
GC [auth JB],
GE [auth KE],
GF [auth LD],
GG [auth MA],
GH [auth MF],
GI [auth ND],
GJ [auth PS],
HC [auth JC],
HD [auth KA],
HE [auth KE],
HF [auth LD],
HG [auth MA],
HH [auth MI],
HI [auth ND],
HJ [auth PT],
IC [auth JC],
ID [auth KA],
IE [auth KF],
IF [auth LD],
IG [auth MB],
II [auth ND],
IJ [auth PU],
JC,
JD [auth KA],
JE [auth KF],
JF [auth LD],
JG [auth MB],
JI [auth NE],
JJ [auth PV],
KC [auth JC],
KD [auth KA],
KE [auth KF],
KF [auth LD],
KG [auth MB],
KI [auth NE],
KJ [auth PW],
LC [auth JC],
LD [auth KA],
LE [auth KF],
LF [auth LD],
LG [auth MB],
LI [auth NE],
LJ [auth PW],
MC [auth JC],
MD [auth KA],
ME [auth KF],
MF [auth LD],
MG [auth MB],
MH [auth NA],
MI [auth NE],
MJ [auth PX],
NC [auth JD],
ND [auth KB],
NE [auth KI],
NF [auth LE],
NG [auth MC],
NH [auth NA],
NI [auth NF],
NJ [auth PX],
OC [auth JD],
OD [auth KB],
OF [auth LE],
OG [auth MC],
OH [auth NA],
OI [auth NF],
PC [auth JD],
PD [auth KB],
PF [auth LE],
PG [auth MC],
PH [auth NA],
PI [auth NF],
QC [auth JD],
QD [auth KB],
QF [auth LE],
QG [auth MD],
QH [auth NA],
QI [auth NF],
RC [auth JD],
RD [auth KB],
RE [auth LA],
RF [auth LE],
RG [auth MD],
RH [auth NB],
RI [auth NI],
SC [auth JE],
SD [auth KC],
SE [auth LA],
SF [auth LF],
SG [auth MD],
SH [auth NB],
TC [auth JE],
TD [auth KC],
TE [auth LA],
TF [auth LF],
TG [auth MD],
TH [auth NB],
UC [auth JE],
UD [auth KC],
UE [auth LA],
UF [auth LF],
UG [auth MD],
UH [auth NB],
VC [auth JE],
VD [auth KC],
VE [auth LA],
VF [auth LF],
VG [auth MD],
VH [auth NB],
WB [auth JA],
WC [auth JE],
WD [auth KD],
WE [auth LA],
WF [auth LI],
WG [auth MD],
WH [auth NB],
WI [auth PM],
XB [auth JA],
XC [auth JF],
XD [auth KD],
XE [auth LB],
XG [auth MD],
XH [auth NC],
XI [auth PM],
YB [auth JA],
YC [auth JF],
YD [auth KD],
YE [auth LB],
YF [auth LJ],
YG [auth ME],
YH [auth NC],
YI [auth PN],
ZB [auth JA],
ZC [auth JF],
ZD [auth KD],
ZE [auth LB],
ZG [auth ME],
ZH [auth NC],
ZI [auth PN]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
HIP
Query on HIP
TA [auth P5],
UA [auth P6],
VA [auth P7],
WA [auth P8],
XA [auth P9]
L-PEPTIDE LINKINGC6 H11 N3 O5 PHIS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.68 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: 2024-10-23
    Type: Initial release
  • Version 1.1: 2025-10-22
    Changes: Data collection, Database references