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Yorodumi- EMDB-3756: Sub-tomogram average of the surface adhesin (NAP) complex from My... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3756 | |||||||||
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Title | Sub-tomogram average of the surface adhesin (NAP) complex from Mycoplasma genitalium cells by cryo-electron tomography. | |||||||||
Map data | Sub-tomogram average of the surface adhesin (NAP) complex from Mycoplasma genitalium cells by cryo-electron tomography. | |||||||||
Sample |
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Biological species | Mycoplasma genitalium G37 (bacteria) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 26.0 Å | |||||||||
Authors | Scheffer MP / Gonzalez-Gonzalez L / Frangakis AS | |||||||||
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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3756.map.gz | 78 KB | EMDB map data format | |
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Header (meta data) | emd-3756-v30.xml emd-3756.xml | 8.6 KB 8.6 KB | Display Display | EMDB header |
Images | emd_3756.png | 86.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3756 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3756 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3756.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sub-tomogram average of the surface adhesin (NAP) complex from Mycoplasma genitalium cells by cryo-electron tomography. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 6.7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Sub-tomogram average of the surface adhesin (NAP) complex from My...
Entire | Name: Sub-tomogram average of the surface adhesin (NAP) complex from Mycoplasma genitalium cells by cryo-electron tomography. |
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Components |
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-Supramolecule #1: Sub-tomogram average of the surface adhesin (NAP) complex from My...
Supramolecule | Name: Sub-tomogram average of the surface adhesin (NAP) complex from Mycoplasma genitalium cells by cryo-electron tomography. type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Mycoplasma genitalium G37 (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.2 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Extraction | Number tomograms: 2 / Number images used: 1500 / Software - Name: MATLAB |
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CTF correction | Software - Name: Super-sampling SART |
Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Super-sampling SART / Number subtomograms used: 1500 |