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- PDB-9mt5: Helical tail assembly of phage JohannRWettstein (Bas63) -

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Basic information

Entry
Database: PDB / ID: 9mt5
TitleHelical tail assembly of phage JohannRWettstein (Bas63)
Components
  • Structural protein
  • Tube protein
KeywordsVIRAL PROTEIN / Tail / sheath / tube / phage / Bas63 / JohannRWettstein
Function / homologyStructural protein ORF10, bacteriophage KPP10 / Protein of unknown function DUF3383 / Bacteriophage PhiTE tail tube protein / Protein of unknown function (DUF3383) / Uncharacterized protein / Structural protein
Function and homology information
Biological speciesEscherichia phage JohannRWettstein (virus)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsHodgkinson-Bean, J.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Agriculture, Forestry and Fisheries (MAFF)GD0696J004 Japan
Japan Society for the Promotion of Science (JSPS)21K20645 Japan
CitationJournal: Sci Adv / Year: 2025
Title: C12 local connector reconstruction of phage JohannRWettstein (Bas63)
Authors: Hodgkinson-Bean, J. / Ayala, R. / McJarrow-Keller, K. / Cassin, L. / Rutter, G.L. / Crowe, A.J.M. / Wolf, M. / Bostina, M.
History
DepositionJan 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tube protein
B: Structural protein


Theoretical massNumber of molelcules
Total (without water)65,1202
Polymers65,1202
Non-polymers00
Water00
1
A: Tube protein
B: Structural protein
x 60


Theoretical massNumber of molelcules
Total (without water)3,907,185120
Polymers3,907,185120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
helical symmetry operation59
2


  • Idetical with deposited unit
  • helical asymmetric unit
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryHelical symmetry: (Circular symmetry: 6 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 10 / Rise per n subunits: 38.1 Å / Rotation per n subunits: 25.9 °)

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Components

#1: Protein Tube protein


Mass: 16203.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia phage JohannRWettstein (virus)
References: UniProt: A0AAE7VV62
#2: Protein Structural protein


Mass: 48916.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia phage JohannRWettstein (virus)
References: UniProt: A0AAE7VVP5
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: JohannRWettstein / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: JohannRWettstein (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Escherichi coli
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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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: 4000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 49.6 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 25.9 ° / Axial rise/subunit: 38.1 Å / Axial symmetry: C6
3D reconstructionResolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 104888 / Symmetry type: HELICAL
RefinementHighest resolution: 3.17 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0023353
ELECTRON MICROSCOPYf_angle_d0.4424563
ELECTRON MICROSCOPYf_dihedral_angle_d4.85462
ELECTRON MICROSCOPYf_chiral_restr0.041538
ELECTRON MICROSCOPYf_plane_restr0.003584

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