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- EMDB-17645: Structure of a heteropolymeric type 4 pilus from a monoderm bacterium -

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Basic information

Entry
Database: EMDB / ID: EMD-17645
TitleStructure of a heteropolymeric type 4 pilus from a monoderm bacterium
Map data
Sample
  • Complex: Type 4 pilus of Streptococcus sanguinis
    • Protein or peptide: Type IV pilin PilE1
KeywordsBacterial pilus Type 4 pilus / PROTEIN FIBRIL
Function / homologyestablishment of competence for transformation / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like / protein secretion by the type II secretion system / type II protein secretion system complex / membrane / Type IV pilin PilE1
Function and homology information
Biological speciesStreptococcus sanguinis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.67 Å
AuthorsAnger R / Pieulle L / Shahin M / Valette O / Le Guenno H / Kosta A / Pelicic V / Fronzes R
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)725554European Union
CitationJournal: Nat Commun / Year: 2023
Title: Structure of a heteropolymeric type 4 pilus from a monoderm bacterium.
Authors: Robin Anger / Laetitia Pieulle / Meriam Shahin / Odile Valette / Hugo Le Guenno / Artemis Kosta / Vladimir Pelicic / Rémi Fronzes /
Abstract: Type 4 pili (T4P) are important virulence factors, which belong to a superfamily of nanomachines ubiquitous in prokaryotes, called type 4 filaments (T4F). T4F are defined as helical polymers of type ...Type 4 pili (T4P) are important virulence factors, which belong to a superfamily of nanomachines ubiquitous in prokaryotes, called type 4 filaments (T4F). T4F are defined as helical polymers of type 4 pilins. Recent advances in cryo-electron microscopy (cryo-EM) led to structures of several T4F, revealing that the long N-terminal α-helix (α1) - the trademark of pilins - packs in the centre of the filaments to form a hydrophobic core. In diderm bacteria - all available bacterial T4F structures are from diderm species - a portion of α1 is melted (unfolded). Here we report that this architecture is conserved in phylogenetically distant monoderm species by determining the structure of Streptococcus sanguinis T4P. Our 3.7 Å resolution cryo-EM structure of S. sanguinis heteropolymeric T4P and the resulting full atomic model including all minor pilins highlight universal features of bacterial T4F and have widespread implications in understanding T4F biology.
History
DepositionJun 15, 2023-
Header (metadata) releaseNov 22, 2023-
Map releaseNov 22, 2023-
UpdateNov 22, 2023-
Current statusNov 22, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17645.png

Downloads & links

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Map

FileDownload / File: emd_17645.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.93 Å
Density
Contour LevelBy AUTHOR: 0.093
Minimum - Maximum-0.11566537 - 0.35453752
Average (Standard dev.)0.00024150473 (±0.012671572)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 297.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_17645_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_17645_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Type 4 pilus of Streptococcus sanguinis

EntireName: Type 4 pilus of Streptococcus sanguinis
Components
  • Complex: Type 4 pilus of Streptococcus sanguinis
    • Protein or peptide: Type IV pilin PilE1

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Supramolecule #1: Type 4 pilus of Streptococcus sanguinis

SupramoleculeName: Type 4 pilus of Streptococcus sanguinis / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Streptococcus sanguinis (bacteria)

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Macromolecule #1: Type IV pilin PilE1

MacromoleculeName: Type IV pilin PilE1 / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Streptococcus sanguinis (bacteria)
Molecular weightTheoretical: 14.752422 KDa
SequenceString:
FTLVELIVVI IIIAIIAAVA IPAITSFQDN ARKSRIQSEH RELVSAIQSY IGAQDDPTNP SEITLAKLAP YMSKNAKNED GIVNSLAKD KSGNSSTSAP GSAHQIDTTN HKLISTFTPS NGGQATVLTY DWSANGVNSN

UniProtKB: Type IV pilin PilE1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.7 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0460000000000003 µm / Nominal defocus min: 0.492 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 203392
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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