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- PDB-8pfb: Structure of a heteropolymeric type 4 pilus from a monoderm bacterium -

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Basic information

Entry
Database: PDB / ID: 8pfb
TitleStructure of a heteropolymeric type 4 pilus from a monoderm bacterium
ComponentsType IV pilin PilE1
KeywordsPROTEIN FIBRIL / Bacterial pilus Type 4 pilus
Function / homology: / establishment of competence for transformation / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like / cell surface / membrane / Type IV pilin PilE1
Function and homology information
Biological speciesStreptococcus sanguinis (bacteria)
MethodELECTRON MICROSCOPY / single 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, 1items
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, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Type IV pilin PilE1
F: Type IV pilin PilE1
C: Type IV pilin PilE1
A: Type IV pilin PilE1
B: Type IV pilin PilE1
I: Type IV pilin PilE1
H: Type IV pilin PilE1
D: Type IV pilin PilE1
E: Type IV pilin PilE1


Theoretical massNumber of molelcules
Total (without water)132,7729
Polymers132,7729
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Type IV pilin PilE1


Mass: 14752.422 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Streptococcus sanguinis (bacteria) / References: UniProt: A0A0B7GU52

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Type 4 pilus of Streptococcus sanguinis / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Streptococcus sanguinis (bacteria)
Buffer solutionpH: 7.6
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: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2046 nm / Nominal defocus min: 492 nm
Image recordingElectron dose: 50.7 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 203392 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0048659
ELECTRON MICROSCOPYf_angle_d0.89211767
ELECTRON MICROSCOPYf_dihedral_angle_d7.7571171
ELECTRON MICROSCOPYf_chiral_restr0.0481432
ELECTRON MICROSCOPYf_plane_restr0.0071511

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