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- PDB-9gs0: Capsid of full Haloferax tailed virus 1 without turret head prote... -

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Basic information

Entry
Database: PDB / ID: 9gs0
TitleCapsid of full Haloferax tailed virus 1 without turret head protein gp31.
Components
  • Capsid stabilization protein
  • Gp30
  • HK97 gp5-like major capsid protein
KeywordsVIRUS / Archaeal virus / turret / capsid
Function / homology: / Capsid stabilization protein / HK97 gp5-like major capsid protein / Gp30
Function and homology information
Biological speciesHaloferax tailed virus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.37 Å
AuthorsZhang, D. / Daum, B. / Isupov, M.N. / McLaren, M. / Stuart, W.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: Sci Adv / Year: 2025
Title: Cryo-EM resolves the structure of the archaeal dsDNA virus HFTV1 from head to tail.
Authors: Daniel X Zhang / Michail N Isupov / Rebecca M Davies / Sabine Schwarzer / Mathew McLaren / William S Stuart / Vicki A M Gold / Hanna M Oksanen / Tessa E F Quax / Bertram Daum /
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 ...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.
History
DepositionSep 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: HK97 gp5-like major capsid protein
AB: HK97 gp5-like major capsid protein
AC: HK97 gp5-like major capsid protein
AD: HK97 gp5-like major capsid protein
AE: HK97 gp5-like major capsid protein
AF: HK97 gp5-like major capsid protein
AI: Capsid stabilization protein
AJ: Capsid stabilization protein
AK: Capsid stabilization protein
AL: Capsid stabilization protein
AM: Capsid stabilization protein
AN: Capsid stabilization protein
AO: Capsid stabilization protein
As: Gp30
At: Gp30
Au: Gp30
Av: Gp30
Aw: Gp30
Ax: Gp30
AG: HK97 gp5-like major capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)474,87871
Polymers473,59420
Non-polymers1,28451
Water00
1
AA: HK97 gp5-like major capsid protein
AB: HK97 gp5-like major capsid protein
AC: HK97 gp5-like major capsid protein
AD: HK97 gp5-like major capsid protein
AE: HK97 gp5-like major capsid protein
AF: HK97 gp5-like major capsid protein
AI: Capsid stabilization protein
AJ: Capsid stabilization protein
AK: Capsid stabilization protein
AL: Capsid stabilization protein
AM: Capsid stabilization protein
AN: Capsid stabilization protein
AO: Capsid stabilization protein
As: Gp30
At: Gp30
Au: Gp30
Av: Gp30
Aw: Gp30
Ax: Gp30
AG: HK97 gp5-like major capsid protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)28,492,6634260
Polymers28,415,6271200
Non-polymers77,0363060
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein
HK97 gp5-like major capsid protein


Mass: 43544.406 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Haloferax tailed virus 1 / References: UniProt: A0A410N6T9
#2: Protein
Capsid stabilization protein


Mass: 13888.911 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Haloferax tailed virus 1 / References: UniProt: A0A410N6Q7
#3: Protein
Gp30 / Gene product 30


Mass: 11926.760 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Haloferax tailed virus 1 / References: UniProt: A0A410N6V5
#4: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Haloferax tailed virus 1 / Type: VIRUS / Entity ID: #1-#3 / Source: NATURAL
Source (natural)Organism: Haloferax tailed virus 1
Details of virusEmpty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Haloferax gibbonsii
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
7Cootmodel fitting
9REFMAC5.8.0267model refinement
10UCSF ChimeraXmodel refinement
11ISOLDEmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2512500 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: RECIPROCAL

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