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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: To Be Published
Title: CryoEM structure of Haloferax tailed virus
Authors: Zhang, D. / Daum, B. / Isupov, M.N. / McLaren, M. / Oksanen, H. / Quax, T.E.F. / Schwarzer, S. / Gold, V.A.M. / Stuart, W.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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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