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Yorodumi- EMDB-12674: Map of the hexameric ESX-5 complex from Mycobacterium xenopi with... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12674 | |||||||||
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Title | Map of the hexameric ESX-5 complex from Mycobacterium xenopi with periplasmic region | |||||||||
Map data | Map of a hexameric ESX-5 complex from Mycobacterium xenopi with periplasmic region | |||||||||
Sample |
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Function / homology | Function and homology information hydrolase activity / ATP hydrolysis activity / DNA binding / ATP binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Mycobacterium xenopi RIVM700367 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.6 Å | |||||||||
Authors | Ritter C / Chojnowski G / Beckham KSH / Mullapudi E / Rettel M / Savitski MM / Mortensen SA / Ziemianowicz D / Kosinski J / Wilmanns M | |||||||||
Citation | Journal: Sci Adv / Year: 2021 Title: Structure of the mycobacterial ESX-5 type VII secretion system pore complex. Authors: Katherine S H Beckham / Christina Ritter / Grzegorz Chojnowski / Daniel S Ziemianowicz / Edukondalu Mullapudi / Mandy Rettel / Mikhail M Savitski / Simon A Mortensen / Jan Kosinski / Matthias Wilmanns / Abstract: The ESX-5 type VII secretion system is a membrane-spanning protein complex key to the virulence of mycobacterial pathogens. However, the overall architecture of the fully assembled translocation ...The ESX-5 type VII secretion system is a membrane-spanning protein complex key to the virulence of mycobacterial pathogens. However, the overall architecture of the fully assembled translocation machinery and the composition of the central secretion pore have remained unknown. Here, we present the high-resolution structure of the 2.1-megadalton ESX-5 core complex. Our structure captured a dynamic, secretion-competent conformation of the pore within a well-defined transmembrane section, sandwiched between two flexible protein layers at the cytosolic entrance and the periplasmic exit. We propose that this flexibility endows the ESX-5 machinery with large conformational plasticity required to accommodate targeted protein secretion. Compared to known secretion systems, a highly dynamic state of the pore may represent a fundamental principle of bacterial secretion machineries. | |||||||||
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_12674.map.gz | 167.8 MB | EMDB map data format | |
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Header (meta data) | emd-12674-v30.xml emd-12674.xml | 12 KB 12 KB | Display Display | EMDB header |
Images | emd_12674.png | 63.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12674 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12674 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_12674.map.gz / Format: CCP4 / Size: 391 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Map of a hexameric ESX-5 complex from Mycobacterium xenopi with periplasmic region | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.29 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 : Hexameric ESX-5 complex from Mycobacterium xenopi: EccB5, EccC5, ...
Entire | Name: Hexameric ESX-5 complex from Mycobacterium xenopi: EccB5, EccC5, EccD5-1, EccD5-2, EccE |
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Components |
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-Supramolecule #1: Hexameric ESX-5 complex from Mycobacterium xenopi: EccB5, EccC5, ...
Supramolecule | Name: Hexameric ESX-5 complex from Mycobacterium xenopi: EccB5, EccC5, EccD5-1, EccD5-2, EccE type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Mycobacterium xenopi RIVM700367 (bacteria) / Location in cell: membrane |
Recombinant expression | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) |
Molecular weight | Theoretical: 2.142 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.2 nm | ||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV |
-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 / Cs: 2.7 mm / Nominal defocus max: -0.7000000000000001 µm / Nominal defocus min: -1.7 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 27873 / Average electron dose: 49.34 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: cryoSPARC (ver. 2.14) |
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Initial angle assignment | Type: OTHER / Software - Name: cryoSPARC (ver. 2.14) |
Final angle assignment | Type: OTHER / Software - Name: cryoSPARC (ver. 2.14) |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.14) / Number images used: 52015 |