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Yorodumi- EMDB-17683: Neisseria meningitidis Type IV pilus SB-GATDH variant bound to th... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17683 | |||||||||
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Title | Neisseria meningitidis Type IV pilus SB-GATDH variant bound to the C24 nanobody | |||||||||
Map data | Raw map of the SB-GATDH variant of Neisseria meningitidis T4P bound to the C24 nanobody | |||||||||
Sample |
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Keywords | Pilin / Extracellular / Adhesion / Aggregation / PROTEIN FIBRIL | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Neisseria meningitidis 8013 (bacteria) / Vicugna pacos (alpaca) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Fernandez-Martinez D / Dumenil G | |||||||||
Funding support | France, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17683.map.gz | 122.2 MB | EMDB map data format | |
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Header (meta data) | emd-17683-v30.xml emd-17683.xml | 19 KB 19 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17683_fsc.xml | 13.2 KB | Display | FSC data file |
Images | emd_17683.png | 41.3 KB | ||
Masks | emd_17683_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-17683.cif.gz | 5.9 KB | ||
Others | emd_17683_additional_1.map.gz emd_17683_half_map_1.map.gz emd_17683_half_map_2.map.gz | 216.8 MB 226.4 MB 226.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17683 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17683 | HTTPS FTP |
-Validation report
Summary document | emd_17683_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_17683_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_17683_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | emd_17683_validation.cif.gz | 28.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17683 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17683 | HTTPS FTP |
-Related structure data
Related structure data | 8pijMC 8p2vC 8p36C 8p3bC 8pizC 8pjpC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_17683.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Raw map of the SB-GATDH variant of Neisseria meningitidis T4P bound to the C24 nanobody | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.93 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17683_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: DL sharpened map of the SB-GATDH variant of...
File | emd_17683_additional_1.map | ||||||||||||
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Annotation | DL sharpened map of the SB-GATDH variant of Neisseria meningitidis T4P bound to the C24 nanobody | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A of the SB-GATDH variant of...
File | emd_17683_half_map_1.map | ||||||||||||
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Annotation | Half map A of the SB-GATDH variant of Neisseria meningitidis T4P bound to the C24 nanobody | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B of the SB-GATDH variant of...
File | emd_17683_half_map_2.map | ||||||||||||
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Annotation | Half map B of the SB-GATDH variant of Neisseria meningitidis T4P bound to the C24 nanobody | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of Neisseria meningitidis PilE SB-GATDH and the C24 nanobody
Entire | Name: Complex of Neisseria meningitidis PilE SB-GATDH and the C24 nanobody |
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Components |
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-Supramolecule #1: Complex of Neisseria meningitidis PilE SB-GATDH and the C24 nanobody
Supramolecule | Name: Complex of Neisseria meningitidis PilE SB-GATDH and the C24 nanobody type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Neisseria meningitidis 8013 (bacteria) |
-Macromolecule #1: Pilin
Macromolecule | Name: Pilin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Neisseria meningitidis 8013 (bacteria) |
Molecular weight | Theoretical: 17.067182 KDa |
Recombinant expression | Organism: Neisseria meningitidis 8013 (bacteria) |
Sequence | String: FTLIELMIVI AIVGILAAVA LPAYQDYTAR AQVSEAILLA EGQKSAVTEY YLNHGEWPGD NSSAGVATSA DIKGKYVQSV TVANGVITA QMASSNVNNE IKSKKLSLWA KRQNGSVKWF CGQPVTRTTA TATDVAAANG KTDDKINTKH LPSTCRDDSS A S UniProtKB: Pilin |
-Macromolecule #2: C24 nanobody
Macromolecule | Name: C24 nanobody / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Vicugna pacos (alpaca) |
Molecular weight | Theoretical: 13.911585 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MAQLQLVESG GGLVQPGGSL RLSCASSGFR SDYYAIVWFR QAPGKEREGV SCISTSGKTT IYADSVKGRF TISRDNAKNT VYLQMNSLK PEDTAVYYCA ADFRGSRLSD VCSYSSMDYW GKGTLATVS |
-Macromolecule #3: SN-GLYCEROL-3-PHOSPHATE
Macromolecule | Name: SN-GLYCEROL-3-PHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: G3P |
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Molecular weight | Theoretical: 172.074 Da |
Chemical component information | ChemComp-G3P: |
-Macromolecule #4: (2~{R})-~{N}-[(2~{R},3~{S},4~{S},5~{R},6~{R})-5-acetamido-2-methy...
Macromolecule | Name: (2~{R})-~{N}-[(2~{R},3~{S},4~{S},5~{R},6~{R})-5-acetamido-2-methyl-4,6-bis(oxidanyl)oxan-3-yl]-2,3-bis(oxidanyl)propanamide type: ligand / ID: 4 / Number of copies: 1 / Formula: WKE |
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Molecular weight | Theoretical: 292.286 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Refinement | Protocol: FLEXIBLE FIT |
Output model | PDB-8pij: |