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- EMDB-29355: Structure of Agrobacterium tumefaciens bacteriophage Milano contr... -

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Basic information

Entry
Database: EMDB / ID: EMD-29355
TitleStructure of Agrobacterium tumefaciens bacteriophage Milano contracted tail-sheath
Map data
Sample
  • Virus: Agrobacterium phage Milano (virus)
    • Protein or peptide: Tail sheath protein
KeywordsMyophage / redox trigger / VIRUS
Function / homologyTail sheath protein
Function and homology information
Biological speciesAgrobacterium phage Milano (virus)
Methodhelical reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsSonani RR / Leiman PG / Wang F / Kreutzberger MAB / Sebastian A / Esteves NC / Kelly RJ / Scharf B / Egelman EH
Funding support United States, 1 items
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, 2023-
Header (metadata) releaseJan 17, 2024-
Map releaseJan 17, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29355.png

Downloads & links

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Map

FileDownload / File: emd_29355.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 512 pix.
= 419.84 Å		0.82 Å/pix.
x 512 pix.
= 419.84 Å		0.82 Å/pix.
x 512 pix.
= 419.84 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.2937687 - 0.57843304
Average (Standard dev.)0.0025412755 (±0.036194146)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 419.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_29355_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_29355_half_map_2.map
Projections & Slices
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Sample components

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Entire : Agrobacterium phage Milano

EntireName: Agrobacterium phage Milano (virus)
Components
  • Virus: Agrobacterium phage Milano (virus)
    • Protein or peptide: Tail sheath protein

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Supramolecule #1: Agrobacterium phage Milano

SupramoleculeName: Agrobacterium phage Milano / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2557550 / Sci species name: Agrobacterium phage Milano / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Agrobacterium fabrum str. C58 (bacteria)

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Macromolecule #1: Tail sheath protein

MacromoleculeName: Tail sheath protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage Milano (virus)
Molecular weightTheoretical: 53.896094 KDa
SequenceString: MAQDALSDGF VRLCIDPSLN FFGEGCKILV EGQMTDDGSA TPDAVTCVTS ELDIIERFGQ GSVLTESLRK VFCTCKSGVS VYALPREDA AAGVKAVYTL TIAGPATTDG RVQLYMGEAE YAVDIGVDAG DTATDIAAAI VAAISPDFPY AATAAAGVIT L TARNAGTI ...String:
MAQDALSDGF VRLCIDPSLN FFGEGCKILV EGQMTDDGSA TPDAVTCVTS ELDIIERFGQ GSVLTESLRK VFCTCKSGVS VYALPREDA AAGVKAVYTL TIAGPATTDG RVQLYMGEAE YAVDIGVDAG DTATDIAAAI VAAISPDFPY AATAAAGVIT L TARNAGTI GNHLSVIYTN LGSCTSVTPE GVTVTFAQTT AGSVNPTPND YATVVNECCF AVYVLSSDDT DWQENLRDWI RS AWDCSKP QCFGHGYVFN KGTLGQVLAD GDNSAELSRL ALPTTYPVLP YLTNAAYGAL SACSTCNNPE LNIQGQTFGL LSC INMPES CTPGWTFGEV TQLQANGFVV SGPSTTSGQG NYTSPYIYND VTNYLRDEKN RPNATFRDAS SRRLAAATGV ALAE FLQQF NGLAVFTKNT NIRTGIIGTN PRLMLGKIRK WAQDNVGTLF SEFDNINEDI QLLTDFEVQP KCVGQPGIFH LNMRY RPPV RGARINVNMA PALFDNCDR

UniProtKB: Tail sheath protein

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 23.93 Å
Applied symmetry - Helical parameters - Δ&Phi: -30.56 °
Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 160399
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8fop

Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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