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- EMDB-17386: Neisseria meningitidis Type IV pilus SA-GATDH variant -

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Basic information

Entry
Database: EMDB / ID: EMD-17386
TitleNeisseria meningitidis Type IV pilus SA-GATDH variant
Map dataRaw map of the SA-GATDH variant of T4P
Sample
  • Complex: PilE variant SA containing GATDH and G3P PTMs
    • Protein or peptide: Fimbrial protein
  • Ligand: SN-GLYCEROL-3-PHOSPHATE
  • Ligand: (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
KeywordsPilin / Extracellular / Adhesion / Aggregation / PROTEIN FIBRIL
Biological speciesNeisseria meningitidis 8013 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsFernandez-Martinez D / Dumenil G
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR 18 CE11 0022 France
CitationJournal: 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
DepositionMay 17, 2023-
Header (metadata) releaseApr 3, 2024-
Map releaseApr 3, 2024-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17386.png

Downloads & links

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Map

FileDownload / File: emd_17386.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRaw map of the SA-GATDH variant of T4P
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 400 pix.
= 384. Å		0.96 Å/pix.
x 400 pix.
= 384. Å		0.96 Å/pix.
x 400 pix.
= 384. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.355
Minimum - Maximum-0.3319263 - 1.1013362
Average (Standard dev.)0.0005390988 (±0.037384607)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 384.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17386_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: DL sharpened map of the SA-GATDH variant of T4P

Fileemd_17386_additional_1.map
AnnotationDL sharpened map of the SA-GATDH variant of T4P
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_17386_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_17386_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PilE variant SA containing GATDH and G3P PTMs

EntireName: PilE variant SA containing GATDH and G3P PTMs
Components
  • Complex: PilE variant SA containing GATDH and G3P PTMs
    • Protein or peptide: Fimbrial protein
  • Ligand: SN-GLYCEROL-3-PHOSPHATE
  • Ligand: (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

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Supramolecule #1: PilE variant SA containing GATDH and G3P PTMs

SupramoleculeName: PilE variant SA containing GATDH and G3P PTMs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Neisseria meningitidis 8013 (bacteria)

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Macromolecule #1: Fimbrial protein

MacromoleculeName: Fimbrial protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Neisseria meningitidis 8013 (bacteria)
Molecular weightTheoretical: 17.054115 KDa
SequenceString:
FTLIELMIVI AIVGILAAVA LPAYQDYTAR AQVSEAILLA EGQKSAVTEY YLNHGEWPGD NSSAGVATSA DIKGKYVKEV EVKNGVITA QMASSNVNNE IKGKKLSLWA KRQDGSVKWF CGLPVARDDT DSATDVKADT TDNINTKHLP STCRDDSSAS

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Macromolecule #2: SN-GLYCEROL-3-PHOSPHATE

MacromoleculeName: SN-GLYCEROL-3-PHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: G3P
Molecular weightTheoretical: 172.074 Da
Chemical component information

ChemComp-G3P:
SN-GLYCEROL-3-PHOSPHATE

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Macromolecule #3: (2~{R})-~{N}-[(2~{R},3~{S},4~{S},5~{R},6~{R})-5-acetamido-2-methy...

MacromoleculeName: (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: 3 / Number of copies: 1 / Formula: WKE
Molecular weightTheoretical: 292.286 Da

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.01 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 10.446 Å
Applied symmetry - Helical parameters - Δ&Phi: 100.612 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1127987
Startup modelType of model: INSILICO MODEL / In silico model: AlphaFold prediction
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-8p3b:
Neisseria meningitidis Type IV pilus SA-GATDH variant

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