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- EMDB-10260: Structure the Nap adhesion complex from the human pathogen Mycopl... -

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Basic information

Entry
Database: EMDB / ID: EMD-10260
TitleStructure the Nap adhesion complex from the human pathogen Mycoplasma genitalium by single particle cryo-EM.
Map dataStructure of the Nap adhesion complex from the human pathogen Mycoplasma genitalium by single particle cryo-EM.
Sample
  • Complex: The Nap adhesin complex from Mycoplasma genitalium by single particle cryo-EM.
Biological speciesMycoplasma genitalium G37 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.0 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) releaseJun 24, 2020-
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: 0.0065
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0065
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10260.png

Downloads & links

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Map

FileDownload / File: emd_10260.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the Nap adhesion complex from the human pathogen Mycoplasma genitalium by single particle cryo-EM.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 300 pix.
= 315. Å		1.05 Å/pix.
x 300 pix.
= 315. Å		1.05 Å/pix.
x 300 pix.
= 315. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0065 / Movie #1: 0.0065
Minimum - Maximum-0.009772225 - 0.01961289
Average (Standard dev.)0.00017136257 (±0.0016804282)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 315.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z315.000315.000315.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0100.0200.000

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Supplemental data

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Sample components

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Entire : The Nap adhesin complex from Mycoplasma genitalium by single part...

EntireName: The Nap adhesin complex from Mycoplasma genitalium by single particle cryo-EM.
Components
  • Complex: The Nap adhesin complex from Mycoplasma genitalium by single particle cryo-EM.

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Supramolecule #1: The Nap adhesin complex from Mycoplasma genitalium by single part...

SupramoleculeName: The Nap adhesin complex from Mycoplasma genitalium by single particle cryo-EM.
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mycoplasma genitalium G37 (bacteria)
Recombinant expressionOrganism: Mycoplasma 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / 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

Particle selectionNumber selected: 160203
CTF correctionSoftware - Name: RELION (ver. 3)
Startup modelType of model: EMDB MAP
EMDB ID:

10259

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 5612
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3)
Final 3D classificationNumber classes: 6 / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model(PDB ID:

6r41

,

6rut

)
RefinementProtocol: RIGID BODY FIT

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