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- EMDB-28657: Agrobacterium tumefaciens Tpilus -

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Basic information

Entry
Database: EMDB / ID: EMD-28657
TitleAgrobacterium tumefaciens Tpilus
Map data
Sample
  • Organelle or cellular component: T-pilus Filament (VirB2 pilin subunit)
    • Protein or peptide: Protein virB2
  • Ligand: (14S,17R)-20-amino-17-hydroxy-11,17-dioxo-12,16,18-trioxa-17lambda~5~-phosphaicosan-14-yl tetradecanoate
KeywordsT-pilus / PROTEIN FIBRIL
Function / homologyConjugal transfer TrbC/type IV secretion VirB2 / TrbC/VIRB2 pilin / type IV secretion system complex / protein secretion by the type IV secretion system / cell outer membrane / Protein virB2
Function and homology information
Biological speciesAgrobacterium fabrum str. C58 (bacteria) / Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsBeltran LC / 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: 2023
Title: Archaeal DNA-import apparatus is homologous to bacterial conjugation machinery.
Authors: Leticia C Beltran / Virginija Cvirkaite-Krupovic / Jessalyn Miller / Fengbin Wang / Mark A B Kreutzberger / Jonasz B Patkowski / Tiago R D Costa / Stefan Schouten / Ilya Levental / Vincent P ...Authors: Leticia C Beltran / Virginija Cvirkaite-Krupovic / Jessalyn Miller / Fengbin Wang / Mark A B Kreutzberger / Jonasz B Patkowski / Tiago R D Costa / Stefan Schouten / Ilya Levental / Vincent P Conticello / Edward H Egelman / Mart Krupovic /
Abstract: Conjugation is a major mechanism of horizontal gene transfer promoting the spread of antibiotic resistance among human pathogens. It involves establishing a junction between a donor and a recipient ...Conjugation is a major mechanism of horizontal gene transfer promoting the spread of antibiotic resistance among human pathogens. It involves establishing a junction between a donor and a recipient cell via an extracellular appendage known as the mating pilus. In bacteria, the conjugation machinery is encoded by plasmids or transposons and typically mediates the transfer of cognate mobile genetic elements. Much less is known about conjugation in archaea. Here, we determine atomic structures by cryo-electron microscopy of three conjugative pili, two from hyperthermophilic archaea (Aeropyrum pernix and Pyrobaculum calidifontis) and one encoded by the Ti plasmid of the bacterium Agrobacterium tumefaciens, and show that the archaeal pili are homologous to bacterial mating pili. However, the archaeal conjugation machinery, known as Ced, has been 'domesticated', that is, the genes for the conjugation machinery are encoded on the chromosome rather than on mobile genetic elements, and mediates the transfer of cellular DNA.
History
DepositionOct 25, 2022-
Header (metadata) releaseMar 22, 2023-
Map releaseMar 22, 2023-
UpdateSep 25, 2024-
Current statusSep 25, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28657.png

Downloads & links

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Map

FileDownload / File: emd_28657.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 300 pix.
= 324. Å		1.08 Å/pix.
x 300 pix.
= 324. Å		1.08 Å/pix.
x 300 pix.
= 324. Å

Surface

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Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.282
Minimum - Maximum-0.53838265 - 1.3855786
Average (Standard dev.)0.006530304 (±0.053043727)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-150-150-150
Dimensions300300300
Spacing300300300
CellA=B=C: 324.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_28657_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_28657_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : T-pilus Filament (VirB2 pilin subunit)

EntireName: T-pilus Filament (VirB2 pilin subunit)
Components
  • Organelle or cellular component: T-pilus Filament (VirB2 pilin subunit)
    • Protein or peptide: Protein virB2
  • Ligand: (14S,17R)-20-amino-17-hydroxy-11,17-dioxo-12,16,18-trioxa-17lambda~5~-phosphaicosan-14-yl tetradecanoate

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Supramolecule #1: T-pilus Filament (VirB2 pilin subunit)

SupramoleculeName: T-pilus Filament (VirB2 pilin subunit) / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Filaments generated by shearing off of bacteria
Source (natural)Organism: Agrobacterium fabrum str. C58 (bacteria) / Location in cell: extracellular

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Macromolecule #1: Protein virB2

MacromoleculeName: Protein virB2 / type: protein_or_peptide / ID: 1 / Number of copies: 40 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria)
Strain: C58 / ATCC 33970
Molecular weightTheoretical: 6.803045 KDa
SequenceString:
GGTDPATMVN NICTFILGPF GQSLAVLGIV AIGISWMFGR ASLGLVAGVV GGIVIMFGAS FLGKTLTGG

UniProtKB: Protein virB2

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Macromolecule #2: (14S,17R)-20-amino-17-hydroxy-11,17-dioxo-12,16,18-trioxa-17lambd...

MacromoleculeName: (14S,17R)-20-amino-17-hydroxy-11,17-dioxo-12,16,18-trioxa-17lambda~5~-phosphaicosan-14-yl tetradecanoate
type: ligand / ID: 2 / Number of copies: 40 / Formula: X3D
Molecular weightTheoretical: 593.773 Da
Chemical component information

ChemComp-X3D:
(14S,17R)-20-amino-17-hydroxy-11,17-dioxo-12,16,18-trioxa-17lambda~5~-phosphaicosan-14-yl tetradecanoate

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
GridModel: EMS Lacey Carbon / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: LEICA EM GP / Details: blot for 3 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / 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: 13.68 Å
Applied symmetry - Helical parameters - Δ&Phi: 32.45 °
Applied symmetry - Helical parameters - Axial symmetry: C5 (5 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1) / Number images used: 49308
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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