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- PDB-8fou: Structure of Agrobacterium tumefaciens bacteriophage Milano contr... -

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Basic information

Entry
Database: PDB / ID: 8fou
TitleStructure of Agrobacterium tumefaciens bacteriophage Milano contracted tail-tube
ComponentsVirion-associated protein
KeywordsVIRUS / Myophage / redox trigger / disulfides
Function / homologyVirion-associated protein
Function and homology information
Biological speciesAgrobacterium phage Milano (virus)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSonani, R.R. / Leiman, P.G. / Wang, F. / Kreutzberger, M.A.B. / Sebastian, A. / Esteves, N.C. / Kelly, R.J. / Scharf, B. / Egelman, E.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
CitationJournal: Nat Commun / Year: 2024
Title: An extensive disulfide bond network prevents tail contraction in Agrobacterium tumefaciens phage Milano.
Authors: Ravi R Sonani / Lee K Palmer / Nathaniel C Esteves / Abigail A Horton / Amanda L Sebastian / Rebecca J Kelly / Fengbin Wang / Mark A B Kreutzberger / William K Russell / Petr G Leiman / ...Authors: Ravi R Sonani / Lee K Palmer / Nathaniel C Esteves / Abigail A Horton / Amanda L Sebastian / Rebecca J Kelly / Fengbin Wang / Mark A B Kreutzberger / William K Russell / Petr G Leiman / Birgit E Scharf / Edward H Egelman /
Abstract: A contractile sheath and rigid tube assembly is a widespread apparatus used by bacteriophages, tailocins, and the bacterial type VI secretion system to penetrate cell membranes. In this mechanism, ...A contractile sheath and rigid tube assembly is a widespread apparatus used by bacteriophages, tailocins, and the bacterial type VI secretion system to penetrate cell membranes. In this mechanism, contraction of an external sheath powers the motion of an inner tube through the membrane. The structure, energetics, and mechanism of the machinery imply rigidity and straightness. The contractile tail of Agrobacterium tumefaciens bacteriophage Milano is flexible and bent to varying degrees, which sets it apart from other contractile tail-like systems. Here, we report structures of the Milano tail including the sheath-tube complex, baseplate, and putative receptor-binding proteins. The flexible-to-rigid transformation of the Milano tail upon contraction can be explained by unique electrostatic properties of the tail tube and sheath. All components of the Milano tail, including sheath subunits, are crosslinked by disulfides, some of which must be reduced for contraction to occur. The putative receptor-binding complex of Milano contains a tailspike, a tail fiber, and at least two small proteins that form a garland around the distal ends of the tailspikes and tail fibers. Despite being flagellotropic, Milano lacks thread-like tail filaments that can wrap around the flagellum, and is thus likely to employ a different binding mechanism.
History
DepositionJan 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Database references / Category: citation / citation_author
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
I: Virion-associated protein


Theoretical massNumber of molelcules
Total (without water)14,6731
Polymers14,6731
Non-polymers00
Water00
1
I: Virion-associated protein
x 24


Theoretical massNumber of molelcules
Total (without water)352,16224
Polymers352,16224
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
helical symmetry operation23
2


  • Idetical with deposited unit
  • helical asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryHelical symmetry: (Circular symmetry: 6 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 24 / Rise per n subunits: 34.07 Å / Rotation per n subunits: 28.21 °)

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Components

#1: Protein Virion-associated protein / Tail-tube / gp21


Mass: 14673.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage Milano (virus) / References: UniProt: A0A482MHE7

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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: Agrobacterium phage Milano / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Agrobacterium phage Milano (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Agrobacterium tumefaciens C58
Buffer solutionpH: 7.4
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: 2400 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 28.21 ° / Axial rise/subunit: 34.07 Å / Axial symmetry: C6
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 160399 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003985
ELECTRON MICROSCOPYf_angle_d0.5041346
ELECTRON MICROSCOPYf_dihedral_angle_d3.909133
ELECTRON MICROSCOPYf_chiral_restr0.045163
ELECTRON MICROSCOPYf_plane_restr0.004178

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