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Yorodumi- PDB-7np7: Structure of an intact ESX-5 inner membrane complex, Composite C1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7np7 | |||||||||||||||
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Title | Structure of an intact ESX-5 inner membrane complex, Composite C1 model | |||||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / T7SS / mycobacteria / protein transport / secretion / type VII secretion system / membrane | |||||||||||||||
Function / homology | Function and homology information 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 hydrolysis activity / DNA binding / ATP binding / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.03 Å | |||||||||||||||
Authors | Fahrenkamp, D. / Bunduc, C.M. / Wald, J. / Ummels, R. / Bitter, W. / Houben, E.N.G. / Marlovits, T.C. | |||||||||||||||
Funding support | Germany, Netherlands, European Union, 4items
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Citation | Journal: Nature / Year: 2021 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 |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7np7.cif.gz | 3.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7np7.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7np7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7np7_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7np7_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7np7_validation.xml.gz | 273.1 KB | Display | |
Data in CIF | 7np7_validation.cif.gz | 435.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/7np7 ftp://data.pdbj.org/pub/pdb/validation_reports/np/7np7 | HTTPS FTP |
-Related structure data
Related structure data | 12514MC 7nprC 7npsC 7nptC 7npuC 7npvC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 53769.988 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: eccB5, Rv1782 Production host: Mycolicibacterium smegmatis MC2 155 (bacteria) References: UniProt: P9WNQ9, Hydrolases; Acting on acid anhydrides #2: Protein | Mass: 152900.750 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: eccC5, Rv1783 Production host: Mycolicibacterium smegmatis MC2 155 (bacteria) References: UniProt: P9WNA5 #3: Protein | Mass: 53480.906 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: eccD5, Rv1795 Production host: Mycolicibacterium smegmatis MC2 155 (bacteria) References: UniProt: P9WNP9 #4: Protein | Mass: 60074.211 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: mycP5, Rv1796, LH57_09820 Production host: Mycolicibacterium smegmatis MC2 155 (bacteria) References: UniProt: O53945, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Intact ESX-5 inner membrane complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 2.32 MDa / Experimental value: NO |
Source (natural) | Organism: Mycobacterium tuberculosis H37Rv (bacteria) |
Source (recombinant) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 59.5 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||
3D reconstruction | Resolution: 4.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 154929 / Symmetry type: POINT |