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- EMDB-3753: Negative stain 3D single particle reconstruction of the isolated ... -

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Entry
Database: EMDB / ID: 3753
TitleNegative stain 3D single particle reconstruction of the isolated surface adhesin P140/P110 complex of Mycoplasma genitalium.
Map dataNegative stain 3D single particle reconstruction of the isolated surface adhesin P140/P110 complex of Mycoplasma genitalium.
SampleNegative stain 3D single particle reconstruction of the isolated surface adhesin P140/P110 complex of Mycoplasma genitalium.:
SourceMycoplasma genitalium G37 (bacteria)
Methodsingle particle reconstruction / 19 Å resolution
AuthorsScheffer MP
CitationJournal: Mol. Microbiol. / Year: 2017
Title: Structural characterization of the NAP; the major adhesion complex of the human pathogen Mycoplasma genitalium.
Authors: Margot P Scheffer / Luis Gonzalez-Gonzalez / Anja Seybert / Mercè Ratera / Michael Kunz / José M Valpuesta / Ignacio Fita / Enrique Querol / Jaume Piñol / Jaime Martín-Benito / Achilleas S Frangakis
Abstract: Mycoplasma genitalium, the causative agent of non-gonococcal urethritis and pelvic inflammatory disease in humans, is a small eubacterium that lacks a peptidoglycan cell wall. On the surface of its ...Mycoplasma genitalium, the causative agent of non-gonococcal urethritis and pelvic inflammatory disease in humans, is a small eubacterium that lacks a peptidoglycan cell wall. On the surface of its plasma membrane is the major surface adhesion complex, known as NAP that is essential for adhesion and gliding motility of the organism. Here, we have performed cryo-electron tomography of intact cells and detergent permeabilized M. genitalium cell aggregates, providing sub-tomogram averages of free and cell-attached NAPs respectively, revealing a tetrameric complex with two-fold rotational (C2) symmetry. Each NAP has two pairs of globular lobes (named α and β lobes), arranged as a dimer of heterodimers with each lobe connected by a stalk to the cell membrane. The β lobes are larger than the α lobes by 20%. Classification of NAPs showed that the complex can tilt with respect to the cell membrane. A protein complex containing exclusively the proteins P140 and P110, was purified from M. genitalium and was structurally characterized by negative-stain single particle EM reconstruction. The close structural similarity found between intact NAPs and the isolated P140/P110 complexes, shows that dimers of P140/P110 heterodimers are the only components of the extracellular region of intact NAPs in M. genitalium.
DateDeposition: Jun 6, 2017 / Header (metadata) release: Jul 26, 2017 / Map release: Jul 26, 2017 / Last update: Sep 13, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1047
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.1047
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3753.map.gz (map file in CCP4 format, 1049 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
64 pix
4.32 Å/pix.
= 276.48 Å
64 pix
4.32 Å/pix.
= 276.48 Å
64 pix
4.32 Å/pix.
= 276.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.32 Å
Density
Contour Level:0.1047 (by author), 0.1047 (movie #1):
Minimum - Maximum-0.16509591 - 0.3144459
Average (Standard dev.)-3.4514454E-5 (0.031377893)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions646464
Origin000
Limit636363
Spacing646464
CellA=B=C: 276.48 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.324.324.32
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z276.480276.480276.480
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS646464
D min/max/mean-0.1650.314-0.000

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Supplemental data

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Sample components

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Entire Negative stain 3D single particle reconstruction of the isolated ...

EntireName: Negative stain 3D single particle reconstruction of the isolated surface adhesin P140/P110 complex of Mycoplasma genitalium.
Details: NAP complexes were extracted from the cell membranes of a modified M. genitalium G37 strain by using the detergent n-octyl-beta-D-glucopyranoside, where gene mg192 had been extended to include a region coding for a six-histidines tag at the C-terminus end of the P110 protein, the gene product of mg192.
Number of components: 1

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Component #1: protein, Negative stain 3D single particle reconstruction of the ...

ProteinName: Negative stain 3D single particle reconstruction of the isolated surface adhesin P140/P110 complex of Mycoplasma genitalium.
Details: NAP complexes were extracted from the cell membranes of a modified M. genitalium G37 strain by using the detergent n-octyl-beta-D-glucopyranoside, where gene mg192 had been extended to include a region coding for a six-histidines tag at the C-terminus end of the P110 protein, the gene product of mg192.
Recombinant expression: No
SourceSpecies: Mycoplasma genitalium G37 (bacteria)
Source (engineered)Expression System: Mycoplasma genitalium G37 (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle
Sample solutionpH: 7.4
VitrificationCryogen name: NONE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 100 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: SIDE ENTRY, EUCENTRIC
CameraDetector: FEI EAGLE (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 14375
3D reconstructionSoftware: RELION / Resolution: 19 Å / Resolution method: FSC 0.143 CUT-OFF

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