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- EMDB-18414: Single particle cryo-EM of the Nap adhesion complex of Mycoplasma... -

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Basic information

Entry
Database: EMDB / ID: EMD-18414
TitleSingle particle cryo-EM of the Nap adhesion complex of Mycoplasma genitalium soaked with 6'-SL at 7.7 Angstrom resolution.
Map data
Sample
  • Complex: Nap adhesion complex soaked with 6-SL
KeywordsAdhesion / Mycoplasma genitalium / CELL ADHESION
Biological speciesMycoplasmoides genitalium G37 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.7 Å
AuthorsSprankel L / Scheffer MP / Frangakis AS
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)FR 1653/6-3 Germany
German Research Foundation (DFG)GRK 2566/1 Germany
CitationJournal: PLoS Pathog / Year: 2023
Title: Cryo-electron tomography reveals the binding and release states of the major adhesion complex from Mycoplasma genitalium.
Authors: Lasse Sprankel / Margot P Scheffer / Sina Manger / Utz H Ermel / Achilleas S Frangakis /
Abstract: The nap particle is an immunogenic surface adhesion complex from Mycoplasma genitalium. It is essential for motility and responsible for binding sialylated oligosaccharides on the surface of the host ...The nap particle is an immunogenic surface adhesion complex from Mycoplasma genitalium. It is essential for motility and responsible for binding sialylated oligosaccharides on the surface of the host cell. The nap particle is composed of two P140-P110 heterodimers, the structure of which was recently solved. However, the interpretation of the mechanism by which the mycoplasma cells orchestrate adhesion remained challenging. Here, we provide cryo-electron tomography structures at ~11 Å resolution, which allow for the distinction between the bound and released state of the nap particle, displaying the in vivo conformational states. Fitting of the atomically resolved structures reveals that bound sialylated oligosaccharides are stabilized by both P110 and P140. Movement of the stalk domains allows for the transfer of conformational changes from the interior of the cell to the binding pocket, thus having the capability of an active release process. It is likely that the same mechanism can be transferred to other Mycoplasma species that belong to the pneumoniae cluster.
History
DepositionSep 8, 2023-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateNov 22, 2023-
Current statusNov 22, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18414.png

Downloads & links

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Map

FileDownload / File: emd_18414.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.674 Å
Density
Contour LevelBy AUTHOR: 0.0921
Minimum - Maximum-0.26259622 - 0.45990998
Average (Standard dev.)0.0022855627 (±0.01988245)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions208208208
Spacing208208208
CellA=B=C: 348.19202 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_18414_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_18414_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Nap adhesion complex soaked with 6-SL

EntireName: Nap adhesion complex soaked with 6-SL
Components
  • Complex: Nap adhesion complex soaked with 6-SL

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Supramolecule #1: Nap adhesion complex soaked with 6-SL

SupramoleculeName: Nap adhesion complex soaked with 6-SL / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mycoplasmoides genitalium G37 (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.025 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 50318
FSC plot (resolution estimation)

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