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- EMDB-10259: Sub-tomogram average of the Nap adhesion complex from the human p... -

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Basic information

Entry
Database: EMDB / ID: EMD-10259
TitleSub-tomogram average of the Nap adhesion complex from the human pathogen Mycoplasma genitalium.
Map dataSub-tomogram average of the surface adhesin (NAP) complex from Mycoplasma genitalium cells by cryo-electron tomography.
Sample
  • Complex: Sub-tomogram average of the Nap adhesin from Mycoplasma genitalium cells.
Biological speciesMycoplasma genitalium G37 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 15.0 Å
AuthorsScheffer MP / Aparicio D
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research FoundationFR1653/6-1 Germany
German Research FoundationSFB902 Germany
CitationJournal: Nat Commun / Year: 2020
Title: Structure and mechanism of the Nap adhesion complex from the human pathogen Mycoplasma genitalium.
Authors: David Aparicio / Margot P Scheffer / Marina Marcos-Silva / David Vizarraga / Lasse Sprankel / Mercè Ratera / Miriam S Weber / Anja Seybert / Sergi Torres-Puig / Luis Gonzalez-Gonzalez / ...Authors: David Aparicio / Margot P Scheffer / Marina Marcos-Silva / David Vizarraga / Lasse Sprankel / Mercè Ratera / Miriam S Weber / Anja Seybert / Sergi Torres-Puig / Luis Gonzalez-Gonzalez / Julian Reitz / Enrique Querol / Jaume Piñol / Oscar Q Pich / Ignacio Fita / Achilleas S Frangakis /
Abstract: Mycoplasma genitalium is a human pathogen adhering to host target epithelial cells and causing urethritis, cervicitis and pelvic inflammatory disease. Essential for infectivity is a transmembrane ...Mycoplasma genitalium is a human pathogen adhering to host target epithelial cells and causing urethritis, cervicitis and pelvic inflammatory disease. Essential for infectivity is a transmembrane adhesion complex called Nap comprising proteins P110 and P140. Here we report the crystal structure of P140 both alone and in complex with the N-terminal domain of P110. By cryo-electron microscopy (cryo-EM) and tomography (cryo-ET) we find closed and open Nap conformations, determined at 9.8 and 15 Å, respectively. Both crystal structures and the cryo-EM structure are found in a closed conformation, where the sialic acid binding site in P110 is occluded. By contrast, the cryo-ET structure shows an open conformation, where the binding site is accessible. Structural information, in combination with functional studies, suggests a mechanism for attachment and release of M. genitalium to and from the host cell receptor, in which Nap conformations alternate to sustain motility and guarantee infectivity.
History
DepositionAug 26, 2019-
Header (metadata) releaseDec 11, 2019-
Map releaseJun 24, 2020-
UpdateJun 24, 2020-
Current statusJun 24, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0117
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0117
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10259.png

Downloads & links

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Map

FileDownload / File: emd_10259.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSub-tomogram average of the surface adhesin (NAP) complex from Mycoplasma genitalium cells by cryo-electron tomography.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.2 Å/pix.
x 128 pix.
= 281.6 Å		2.2 Å/pix.
x 128 pix.
= 281.6 Å		2.2 Å/pix.
x 128 pix.
= 281.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0117 / Movie #1: 0.0117
Minimum - Maximum0 - 0.022023555
Average (Standard dev.)0.010204303 (±0.0008645539)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.22.22.2
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z281.600281.600281.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean0.0000.0220.010

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Supplemental data

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Sample components

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Entire : Sub-tomogram average of the Nap adhesin from Mycoplasma genitaliu...

EntireName: Sub-tomogram average of the Nap adhesin from Mycoplasma genitalium cells.
Components
  • Complex: Sub-tomogram average of the Nap adhesin from Mycoplasma genitalium cells.

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Supramolecule #1: Sub-tomogram average of the Nap adhesin from Mycoplasma genitaliu...

SupramoleculeName: Sub-tomogram average of the Nap adhesin from Mycoplasma genitalium cells.
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mycoplasma genitalium G37 (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE
DetailsMildly detergent-lysed cells

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 8800
ExtractionNumber tomograms: 54 / Number images used: 11000
CTF correctionSoftware - Name: Super-sampling SART (ver. 2)
Software - details: Kunz, M. & Frangakis, A. S. Three-dimensional CTF correction improves the resolution of electron tomograms. Journal of structural biology 197, 114-122, doi: 10.1016
Details: Tomograms were reconstructed by super-sampling SART with 3D contrast transfer function (CTF) correction.
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

Initial model(PDB ID:

6r41

,

6rut

)
RefinementProtocol: RIGID BODY FIT

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