[English] 日本語
Yorodumi- EMDB-3753: Negative stain 3D single particle reconstruction of the isolated ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3753 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Negative stain 3D single particle reconstruction of the isolated surface adhesin P140/P110 complex of Mycoplasma genitalium. | |||||||||
Map data | Negative stain 3D single particle reconstruction of the isolated surface adhesin P140/P110 complex of Mycoplasma genitalium. | |||||||||
Sample |
| |||||||||
Biological species | Mycoplasma genitalium G37 (bacteria) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 19.0 Å | |||||||||
Authors | Scheffer MP | |||||||||
Citation | Journal: 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3753.map.gz | 954.5 KB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-3753-v30.xml emd-3753.xml | 8.8 KB 8.8 KB | Display Display | EMDB header |
Images | emd_3753.png | 78.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3753 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3753 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_3753.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Negative stain 3D single particle reconstruction of the isolated surface adhesin P140/P110 complex of Mycoplasma genitalium. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Negative stain 3D single particle reconstruction of the isolated ...
Entire | Name: Negative stain 3D single particle reconstruction of the isolated surface adhesin P140/P110 complex of Mycoplasma genitalium. |
---|---|
Components |
|
-Supramolecule #1: Negative stain 3D single particle reconstruction of the isolated ...
Supramolecule | Name: 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 expression | Organism: Mycoplasma genitalium G37 (bacteria) |
Molecular weight | Experimental: 495 kDa/nm |
-Experimental details
-Structure determination
Method | negative staining |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
---|---|
Staining | Type: NEGATIVE / Material: Uranyl Acetate |
-Electron microscopy
Microscope | FEI TECNAI F20 |
---|---|
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
Image recording | Film or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 100.0 e/Å2 |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Final angle assignment | Type: NOT APPLICABLE |
---|---|
Final reconstruction | Applied 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 |