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

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Entry
Database: EMDB / ID: EMD-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.
Sample
  • Complex: Negative stain 3D single particle reconstruction of the isolated surface adhesin P140/P110 complex of Mycoplasma genitalium.
Biological speciesMycoplasma genitalium G37 (bacteria)
Methodsingle particle reconstruction / negative staining / Resolution: 19.0 Å
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.
History
DepositionJun 6, 2017-
Header (metadata) releaseJul 26, 2017-
Map releaseJul 26, 2017-
UpdateSep 13, 2017-
Current statusSep 13, 2017Processing site: PDBe / Status: Released

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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

emd_3753.png

Downloads & links

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Map

FileDownload / File: emd_3753.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain 3D single particle reconstruction of the isolated surface adhesin P140/P110 complex of Mycoplasma genitalium.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.32 Å/pix.
x 64 pix.
= 276.48 Å		4.32 Å/pix.
x 64 pix.
= 276.48 Å		4.32 Å/pix.
x 64 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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1047 / Movie #1: 0.1047
Minimum - Maximum-0.16509591 - 0.3144459
Average (Standard dev.)-0.000034514454 (±0.031377893)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 276.48 Å
α=β=γ: 90.0 °

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
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.
Components
  • Complex: Negative stain 3D single particle reconstruction of the isolated surface adhesin P140/P110 complex of Mycoplasma genitalium.

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Supramolecule #1: Negative stain 3D single particle reconstruction of the isolated ...

SupramoleculeName: Negative stain 3D single particle reconstruction of the isolated surface adhesin P140/P110 complex of Mycoplasma genitalium.
type: complex / ID: 1 / Parent: 0
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 ...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.
Source (natural)Organism: Mycoplasma genitalium G37 (bacteria)
Recombinant expressionOrganism: Mycoplasma genitalium G37 (bacteria)
Molecular weightExperimental: 495 kDa/nm

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
StainingType: NEGATIVE / Material: Uranyl Acetate

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 100.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 14375
Final angle assignmentType: NOT APPLICABLE

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