+Open data
-Basic information
Entry | Database: PDB / ID: 8p36 | ||||||
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Title | Neisseria meningitidis Type IV pilus SB-DATDH variant | ||||||
Components | Neisseria meningitidis PilE, SB-DATDH variant | ||||||
Keywords | PROTEIN FIBRIL / Pilin / Extracellular / Adhesion / Aggregation | ||||||
Function / homology | Chem-B6D / SN-GLYCEROL-3-PHOSPHATE Function and homology information | ||||||
Biological species | Neisseria meningitidis 8013 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.51 Å | ||||||
Authors | Fernandez-Martinez, D. / Dumenil, G. | ||||||
Funding support | France, 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: Cryo-EM structures of type IV pili complexed with nanobodies reveal immune escape mechanisms. Authors: David Fernandez-Martinez / Youxin Kong / Sylvie Goussard / Agustin Zavala / Pauline Gastineau / Martial Rey / Gabriel Ayme / Julia Chamot-Rooke / Pierre Lafaye / Matthijn Vos / Ariel Mechaly ...Authors: David Fernandez-Martinez / Youxin Kong / Sylvie Goussard / Agustin Zavala / Pauline Gastineau / Martial Rey / Gabriel Ayme / Julia Chamot-Rooke / Pierre Lafaye / Matthijn Vos / Ariel Mechaly / Guillaume Duménil / Abstract: Type IV pili (T4P) are prevalent, polymeric surface structures in pathogenic bacteria, making them ideal targets for effective vaccines. However, bacteria have evolved efficient strategies to evade ...Type IV pili (T4P) are prevalent, polymeric surface structures in pathogenic bacteria, making them ideal targets for effective vaccines. However, bacteria have evolved efficient strategies to evade type IV pili-directed antibody responses. Neisseria meningitidis are prototypical type IV pili-expressing Gram-negative bacteria responsible for life threatening sepsis and meningitis. This species has evolved several genetic strategies to modify the surface of its type IV pili, changing pilin subunit amino acid sequence, nature of glycosylation and phosphoforms, but how these modifications affect antibody binding at the structural level is still unknown. Here, to explore this question, we determine cryo-electron microscopy (cryo-EM) structures of pili of different sequence types with sufficiently high resolution to visualize posttranslational modifications. We then generate nanobodies directed against type IV pili which alter pilus function in vitro and in vivo. Cyro-EM in combination with molecular dynamics simulation of the nanobody-pilus complexes reveals how the different types of pili surface modifications alter nanobody binding. Our findings shed light on the impressive complementarity between the different strategies used by bacteria to avoid antibody binding. Importantly, we also show that structural information can be used to make informed modifications in nanobodies as countermeasures to these immune evasion mechanisms. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8p36.cif.gz | 43.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8p36.ent.gz | 27.8 KB | Display | PDB format |
PDBx/mmJSON format | 8p36.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8p36_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8p36_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8p36_validation.xml.gz | 25.7 KB | Display | |
Data in CIF | 8p36_validation.cif.gz | 33.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p3/8p36 ftp://data.pdbj.org/pub/pdb/validation_reports/p3/8p36 | HTTPS FTP |
-Related structure data
Related structure data | 17384MC 8p2vC 8p3bC 8pijC 8pizC 8pjpC 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: 17067.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neisseria meningitidis 8013 (bacteria) |
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#2: Chemical | ChemComp-G3P / |
#3: Sugar | ChemComp-B6D / |
Has ligand of interest | Y |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: PilE variant SB containing DATDH and G3P PTMs / Type: COMPLEX / Entity ID: #1 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Neisseria meningitidis 8013 (bacteria) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 0.01 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 600 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.20.1_4487: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 100.683 ° / Axial rise/subunit: 9.977 Å / Axial symmetry: C1 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.51 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 114167 / Symmetry type: HELICAL | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.51 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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