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- EMDB-12523: Structure of an intact ESX-5 inner membrane complex, EccC5 extended -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12523 | |||||||||||||||
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Title | Structure of an intact ESX-5 inner membrane complex, EccC5 extended | |||||||||||||||
![]() | 3D refinement map. | |||||||||||||||
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Function / homology | ![]() Hydrolases; Acting on acid anhydrides / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / peptidoglycan-based cell wall / protein processing / hydrolase activity / serine-type endopeptidase activity / ATP binding / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.27 Å | |||||||||||||||
![]() | Bunduc CM / Fahrenkamp D / Wald J / Ummels R / Bitter W / Houben ENG / Marlovits TC | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structure and dynamics of a mycobacterial type VII secretion system. Authors: Catalin M Bunduc / Dirk Fahrenkamp / Jiri Wald / Roy Ummels / Wilbert Bitter / Edith N G Houben / Thomas C Marlovits / ![]() ![]() Abstract: Mycobacterium tuberculosis is the cause of one of the most important infectious diseases in humans, which leads to 1.4 million deaths every year. Specialized protein transport systems-known as ...Mycobacterium tuberculosis is the cause of one of the most important infectious diseases in humans, which leads to 1.4 million deaths every year. Specialized protein transport systems-known as type VII secretion systems (T7SSs)-are central to the virulence of this pathogen, and are also crucial for nutrient and metabolite transport across the mycobacterial cell envelope. Here we present the structure of an intact T7SS inner-membrane complex of M. tuberculosis. We show how the 2.32-MDa ESX-5 assembly, which contains 165 transmembrane helices, is restructured and stabilized as a trimer of dimers by the MycP protease. A trimer of MycP caps a central periplasmic dome-like chamber that is formed by three EccB dimers, with the proteolytic sites of MycP facing towards the cavity. This chamber suggests a central secretion and processing conduit. Complexes without MycP show disruption of the EccB periplasmic assembly and increased flexibility, which highlights the importance of MycP for complex integrity. Beneath the EccB-MycP chamber, dimers of the EccC ATPase assemble into three bundles of four transmembrane helices each, which together seal the potential central secretion channel. Individual cytoplasmic EccC domains adopt two distinctive conformations that probably reflect different secretion states. Our work suggests a previously undescribed mechanism of protein transport and provides a structural scaffold to aid in the development of drugs against this major human pathogen. | |||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 193.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15 KB 15 KB | Display Display | ![]() |
Images | ![]() | 88.4 KB | ||
Others | ![]() ![]() | 193.8 MB 193.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7np7C ![]() 7nprC ![]() 7npsC ![]() 7nptC ![]() 7npuC ![]() 7npvC C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 3D refinement map. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Half1 of 3D refinement map.
File | emd_12523_half_map_1.map | ||||||||||||
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Annotation | Half1 of 3D refinement map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half2 of 3D refinement map.
File | emd_12523_half_map_2.map | ||||||||||||
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Annotation | Half2 of 3D refinement map. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Structure of an intact ESX-5 inner membrane complex, EccC5 extended
Entire | Name: Structure of an intact ESX-5 inner membrane complex, EccC5 extended |
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Components |
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-Supramolecule #1: Structure of an intact ESX-5 inner membrane complex, EccC5 extended
Supramolecule | Name: Structure of an intact ESX-5 inner membrane complex, EccC5 extended type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
Molecular weight | Theoretical: 2.32 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 59.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.27 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 149055 |
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Initial angle assignment | Type: OTHER / Details: Rotationally averaged 3D structure. |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |