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- PDB-9h5b: Tail fibre of Haloferax tailed virus 1 -

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Basic information

Entry
Database: PDB / ID: 9h5b
TitleTail fibre of Haloferax tailed virus 1
Components
  • Baseplate hub
  • Tail fiber protein of Haloferax tailed virus 1 gp42
KeywordsVIRUS / Archaeal virus / tail
Function / homologyBaseplate hub / Uncharacterized protein
Function and homology information
Biological speciesHaloferax tailed virus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsZhang, D. / Daum, B. / Isupov, M.N. / McLaren, M.
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
DepositionOct 22, 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
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
BG: Tail fiber protein of Haloferax tailed virus 1 gp42
BH: Tail fiber protein of Haloferax tailed virus 1 gp42
BI: Tail fiber protein of Haloferax tailed virus 1 gp42
BE: Baseplate hub
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,77015
Polymers240,4204
Non-polymers35011
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Tail fiber protein of Haloferax tailed virus 1 gp42


Mass: 45959.707 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Haloferax tailed virus 1 / References: UniProt: A0A410N721
#2: Protein Baseplate hub


Mass: 102541.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloferax tailed virus 1 / References: UniProt: A0A410N6T6
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / 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-#2 / Source: NATURAL
Source (natural)Organism: Haloferax tailed virus 1
Details of virusEmpty: NO / 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 recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
1150TFS FALCON 4i (4k x 4k)
2154.6GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
7Cootmodel fitting
8UCSF ChimeraXmodel fitting
9ISOLDEmodel fitting
11REFMAC5.8.0267model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 336454 / Symmetry type: POINT
RefinementResolution: 3.6→432 Å / Cor.coef. Fo:Fc: 0.817 / SU B: 5.362 / SU ML: 0.081 / ESU R: 0.09
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflection
Rwork0.47458 --
obs0.47458 3618270 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 119.583 Å2
Baniso -1Baniso -2Baniso -3
1-1.61 Å20.05 Å2-0.14 Å2
2--1.16 Å20.14 Å2
3----2.77 Å2
Refinement stepCycle: 1 / Total: 9850
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0030.01210020
ELECTRON MICROSCOPYr_bond_other_d
ELECTRON MICROSCOPYr_angle_refined_deg1.2061.63213734
ELECTRON MICROSCOPYr_angle_other_deg
ELECTRON MICROSCOPYr_dihedral_angle_1_deg10.88351345
ELECTRON MICROSCOPYr_dihedral_angle_2_deg38.45425.273476
ELECTRON MICROSCOPYr_dihedral_angle_3_deg14.119151407
ELECTRON MICROSCOPYr_dihedral_angle_4_deg19.8691530
ELECTRON MICROSCOPYr_chiral_restr0.1010.21426
ELECTRON MICROSCOPYr_gen_planes_refined0.0040.027884
ELECTRON MICROSCOPYr_gen_planes_other
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it2.41511.6865392
ELECTRON MICROSCOPYr_mcbond_other
ELECTRON MICROSCOPYr_mcangle_it4.22217.5316733
ELECTRON MICROSCOPYr_mcangle_other
ELECTRON MICROSCOPYr_scbond_it2.81912.1874628
ELECTRON MICROSCOPYr_scbond_other
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other
ELECTRON MICROSCOPYr_long_range_B_refined10.01214921
ELECTRON MICROSCOPYr_long_range_B_other
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.6→3.694 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork2.324 267542 -
obs--100 %

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