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- EMDB-27414: Cryo-EM structure of conjugation pili from Aeropyrum pernix -

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Basic information

Entry
Database: EMDB / ID: EMD-27414
TitleCryo-EM structure of conjugation pili from Aeropyrum pernix
Map dataConjugation pili from Aeropyrum pernix
Sample
  • Organelle or cellular component: Conjugation pilin protein
    • Protein or peptide: Pilin protein
  • Ligand: (2S)-3-{[(3R,7S,11S,15S)-3,7,11,15,19-pentamethylicosyl]oxy}-2-{[(2R,6S,10S,14R)-2,6,10,14,18-pentamethylnonadecyl]oxy}propyl dihydrogen phosphate
KeywordsArchaeal conjugation pilus / PROTEIN FIBRIL
Function / homology: / membrane / Uncharacterized protein
Function and homology information
Biological speciesAeropyrum pernix (archaea)
Methodhelical reconstruction / cryo EM / Resolution: 3.44 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
DepositionJun 22, 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_27414.png

Downloads & links

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Map

FileDownload / File: emd_27414.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConjugation pili from Aeropyrum pernix
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.138
Minimum - Maximum-0.40478286 - 0.80903393
Average (Standard dev.)0.004112166 (±0.038189486)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Conjugation pili from Aeropyrum pernix

Fileemd_27414_half_map_1.map
AnnotationConjugation pili from Aeropyrum pernix
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Conjugation pili from Aeropyrum pernix

Fileemd_27414_half_map_2.map
AnnotationConjugation pili from Aeropyrum pernix
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Conjugation pilin protein

EntireName: Conjugation pilin protein
Components
  • Organelle or cellular component: Conjugation pilin protein
    • Protein or peptide: Pilin protein
  • Ligand: (2S)-3-{[(3R,7S,11S,15S)-3,7,11,15,19-pentamethylicosyl]oxy}-2-{[(2R,6S,10S,14R)-2,6,10,14,18-pentamethylnonadecyl]oxy}propyl dihydrogen phosphate

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Supramolecule #1: Conjugation pilin protein

SupramoleculeName: Conjugation pilin protein / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Aeropyrum pernix (archaea)

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Macromolecule #1: Pilin protein

MacromoleculeName: Pilin protein / type: protein_or_peptide / ID: 1 / Number of copies: 30 / Enantiomer: LEVO
Source (natural)Organism: Aeropyrum pernix (archaea)
Molecular weightTheoretical: 9.070671 KDa
SequenceString:
AADIVQMVED LTGKLTALAW ALFLLSWSIG WTLRGSPIPS SRIKRVGNSL IEDSMWAALW LALGTTVFAV IVRLAGIVNE VLLG

UniProtKB: Uncharacterized protein

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Macromolecule #2: (2S)-3-{[(3R,7S,11S,15S)-3,7,11,15,19-pentamethylicosyl]oxy}-2-{[...

MacromoleculeName: (2S)-3-{[(3R,7S,11S,15S)-3,7,11,15,19-pentamethylicosyl]oxy}-2-{[(2R,6S,10S,14R)-2,6,10,14,18-pentamethylnonadecyl]oxy}propyl dihydrogen phosphate
type: ligand / ID: 2 / Number of copies: 60 / Formula: RHR
Molecular weightTheoretical: 859.376 Da
Chemical component information

ChemComp-RHR:
(2S)-3-{[(3R,7S,11S,15S)-3,7,11,15,19-pentamethylicosyl]oxy}-2-{[(2R,6S,10S,14R)-2,6,10,14,18-pentamethylnonadecyl]oxy}propyl dihydrogen phosphate

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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
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: LEICA EM GP / Details: blot for 3 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN
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 / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 3.61 Å
Applied symmetry - Helical parameters - Δ&Phi: 76.5 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 44262
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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