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- PDB-8qsi: Portal protein of empty Haloferax tailed virus 1. -

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Basic information

Entry
Database: PDB / ID: 8qsi
TitlePortal protein of empty Haloferax tailed virus 1.
Components
  • HK97 gp6-like/SPP1 gp15-like head-tail connector
  • Portal protein
KeywordsVIRUS / Archaeal virus / portal / portal capsid interface / Mg ions
Function / homologyPortal protein / HK97 gp6-like/SPP1 gp15-like head-tail connector
Function and homology information
Biological speciesHaloferax tailed virus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 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 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2024Provider: 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
PM: HK97 gp6-like/SPP1 gp15-like head-tail connector
PN: HK97 gp6-like/SPP1 gp15-like head-tail connector
PO: HK97 gp6-like/SPP1 gp15-like head-tail connector
PP: HK97 gp6-like/SPP1 gp15-like head-tail connector
PQ: HK97 gp6-like/SPP1 gp15-like head-tail connector
PR: HK97 gp6-like/SPP1 gp15-like head-tail connector
PS: HK97 gp6-like/SPP1 gp15-like head-tail connector
PT: HK97 gp6-like/SPP1 gp15-like head-tail connector
PU: HK97 gp6-like/SPP1 gp15-like head-tail connector
PV: HK97 gp6-like/SPP1 gp15-like head-tail connector
PW: HK97 gp6-like/SPP1 gp15-like head-tail connector
PX: HK97 gp6-like/SPP1 gp15-like head-tail connector
PA: Portal protein
PB: Portal protein
PC: Portal protein
PD: Portal protein
PE: Portal protein
PF: Portal protein
PG: Portal protein
PH: Portal protein
PI: Portal protein
PJ: Portal protein
PK: Portal protein
PL: Portal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,095,49336
Polymers1,095,20124
Non-polymers29212
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
HK97 gp6-like/SPP1 gp15-like head-tail connector


Mass: 15585.868 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Haloferax tailed virus 1 / References: UniProt: A0A410N6S3
#2: Protein
Portal protein


Mass: 75680.906 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Haloferax tailed virus 1 / References: UniProt: A0A410N6Q2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: #2, #1 / 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
2EPU5image acquisition
4RELION4.0-betaCTF correction
7Cootmodel fitting
8UCSF ChimeraXmodel fitting
9ISOLDEmodel fitting
11REFMACmodel refinement
Image processingDetails: Dataset produced as a combination of both FALCON 4i and K3 collections
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C12 (12 fold cyclic)
3D reconstructionResolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7163 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: RECIPROCAL
Atomic model buildingType: in silico model
RefinementResolution: 2.75→2.75 Å / Cor.coef. Fo:Fc: 0.753 / WRfactor Rwork: 0.448 / SU B: 10.117 / SU ML: 0.175 / Average fsc overall: 0.4393 / Average fsc work: 0.4393 / ESU R: 0.096 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rwork0.4484 7971714 -
all0.448 --
Rfree--0 %
obs--100 %
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 75.425 Å2
Baniso -1Baniso -2Baniso -3
1--0.254 Å2-0.008 Å20.006 Å2
2---0.251 Å20.005 Å2
3---0.504 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.01251648
ELECTRON MICROSCOPYr_angle_refined_deg1.6441.64270092
ELECTRON MICROSCOPYr_dihedral_angle_1_deg7.52656456
ELECTRON MICROSCOPYr_dihedral_angle_2_deg32.01323.743048
ELECTRON MICROSCOPYr_dihedral_angle_3_deg12.793158556
ELECTRON MICROSCOPYr_dihedral_angle_4_deg19.96315324
ELECTRON MICROSCOPYr_chiral_restr0.1120.26624
ELECTRON MICROSCOPYr_gen_planes_refined0.0090.0240224
ELECTRON MICROSCOPYr_nbd_refined0.1980.241784
ELECTRON MICROSCOPYr_nbtor_refined0.290.271554
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.070.22496
ELECTRON MICROSCOPYr_metal_ion_refined0.0420.248
ELECTRON MICROSCOPYr_mcbond_it3.817.23125932
ELECTRON MICROSCOPYr_mcangle_it6.94110.82432352
ELECTRON MICROSCOPYr_scbond_it5.0957.66925716
ELECTRON MICROSCOPYr_scangle_it9.0511.22937740
ELECTRON MICROSCOPYr_lrange_it17.342130.567200244
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor Rwork
2.64-2.7090.5885893740.5885893740.1120.588
2.709-2.7830.5875755580.5875755580.1450.587
2.783-2.8640.5515599490.5515599490.1560.551
2.864-2.9520.545421660.545421660.1940.54
2.952-3.0480.5465257700.5465257700.2060.546
3.048-3.1550.5365097690.5365097690.2840.536
3.155-3.2750.5284916490.5284916490.3350.528
3.275-3.4080.5134715790.5134715790.4130.513
3.408-3.560.4924536270.4924536270.4970.492
3.56-3.7330.4724334250.4724334250.5720.472
3.733-3.9350.4384114860.4384114860.6620.438
3.935-4.1740.4143894720.4143894720.7270.414
4.174-4.4620.3913661060.3913661060.7660.391
4.462-4.820.3743412150.3743412150.80.374
4.82-5.280.3713131350.3713131350.7950.371
5.28-5.9030.3962837510.3962837510.7490.396
5.903-6.8160.4332494890.4332494890.6950.433
6.816-8.3470.4042112690.4042112690.7370.404
8.347-11.8020.3791630490.3791630490.7850.379
11.802-412.1920.521891740.521891740.5190.521

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