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Yorodumi- PDB-8pfb: Structure of a heteropolymeric type 4 pilus from a monoderm bacterium -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pfb | ||||||
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Title | Structure of a heteropolymeric type 4 pilus from a monoderm bacterium | ||||||
Components | Type IV pilin PilE1 | ||||||
Keywords | PROTEIN 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 / protein secretion by the type II secretion system / type II protein secretion system complex / membrane / Type IV pilin PilE1 Function and homology information | ||||||
Biological species | Streptococcus sanguinis (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.67 Å | ||||||
Authors | Anger, R. / Pieulle, L. / Shahin, M. / Valette, O. / Le Guenno, H. / Kosta, A. / Pelicic, V. / Fronzes, R. | ||||||
Funding support | European Union, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pfb.cif.gz | 354.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pfb.ent.gz | 296.3 KB | Display | PDB format |
PDBx/mmJSON format | 8pfb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pfb_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8pfb_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8pfb_validation.xml.gz | 44.6 KB | Display | |
Data in CIF | 8pfb_validation.cif.gz | 67.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pf/8pfb ftp://data.pdbj.org/pub/pdb/validation_reports/pf/8pfb | HTTPS FTP |
-Related structure data
Related structure data | 17645MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Type 4 pilus of Streptococcus sanguinis / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Streptococcus sanguinis (bacteria) |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2046 nm / Nominal defocus min: 492 nm |
Image recording | Electron dose: 50.7 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 203392 / Symmetry type: POINT | ||||||||||||||||||||||||
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