+Open data
-Basic information
Entry | Database: PDB / ID: 6umm | ||||||||||||||||||
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Title | A complete structure of the ESX-3 translocon complex | ||||||||||||||||||
Components |
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Keywords | TRANSPORT PROTEIN / ESX / secretion system / type VII secretion system / mycobacteria / complex / membrane protein | ||||||||||||||||||
Function / homology | Function and homology information Hydrolases; Acting on acid anhydrides / hydrolase activity / ATP hydrolysis activity / DNA binding / ATP binding / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | Mycobacterium smegmatis (bacteria) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||||||||
Authors | Poweleit, N. / Rosenberg, O.S. | ||||||||||||||||||
Funding support | United States, 5items
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Citation | Journal: Elife / Year: 2019 Title: The structure of the endogenous ESX-3 secretion system. Authors: Nicole Poweleit / Nadine Czudnochowski / Rachel Nakagawa / Donovan D Trinidad / Kenan C Murphy / Christopher M Sassetti / Oren S Rosenberg / Abstract: The ESX (or Type VII) secretion systems are protein export systems in mycobacteria and many Gram-positive bacteria that mediate a broad range of functions including virulence, conjugation, and ...The ESX (or Type VII) secretion systems are protein export systems in mycobacteria and many Gram-positive bacteria that mediate a broad range of functions including virulence, conjugation, and metabolic regulation. These systems translocate folded dimers of WXG100-superfamily protein substrates across the cytoplasmic membrane. We report the cryo-electron microscopy structure of an ESX-3 system, purified using an epitope tag inserted with recombineering into the chromosome of the model organism . The structure reveals a stacked architecture that extends above and below the inner membrane of the bacterium. The ESX-3 protomer complex is assembled from a single copy of the EccB, EccC, and EccE and two copies of the EccD protein. In the structure, the protomers form a stable dimer that is consistent with assembly into a larger oligomer. The ESX-3 structure provides a framework for further study of these important bacterial transporters. | ||||||||||||||||||
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 | 6umm.cif.gz | 513.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6umm.ent.gz | 422.5 KB | Display | PDB format |
PDBx/mmJSON format | 6umm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6umm_validation.pdf.gz | 421.5 KB | Display | wwPDB validaton report |
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Full document | 6umm_full_validation.pdf.gz | 467.5 KB | Display | |
Data in XML | 6umm_validation.xml.gz | 61 KB | Display | |
Data in CIF | 6umm_validation.cif.gz | 93.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/um/6umm ftp://data.pdbj.org/pub/pdb/validation_reports/um/6umm | HTTPS FTP |
-Related structure data
Related structure data | 20820MC 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: 30813.355 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QQ48 #2: Protein | Mass: 48292.480 Da / Num. of mol.: 4 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QQ46 #3: Protein | Mass: 9145.638 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 References: UniProt: A0QQ39, Hydrolases; Acting on acid anhydrides #4: Protein | Mass: 44898.371 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QQ40 |
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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: ESX-3 translocon complex / Type: COMPLEX / Entity ID: all / Source: NATURAL | ||||||||||||||||||||
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Molecular weight | Value: 0.66 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 | ||||||||||||||||||||
Buffer solution | pH: 8 Details: Solutions were made fresh and filter-sterilized before use. | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 5.52 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 73.5 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 7337 |
-Processing
Software | Name: PHENIX / Version: 1.16_3549: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 778149 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90479 / Algorithm: BACK PROJECTION / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||
Refine LS restraints |
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