|Entry||Database: PDB / ID: 6sgy|
|Title||Structure of EccB3 dimer from the ESX-3 core complex|
|Components||ESX-3 secretion system protein EccB3|
|Keywords||MEMBRANE PROTEIN / Type VII Secretion System ESX-3 secretion system T7SS ESX-3 Mycobacterium smegmatis|
|Function / homology||Type VII secretion system EccB, repeat 3 domain / Type VII secretion system EccB / Hydrolases; Acting on acid anhydrides / hydrolase activity / integral component of membrane / ATP binding / plasma membrane / ESX-3 secretion system ATPase EccB3|
Function and homology information
|Biological species||Mycobacterium smegmatis (bacteria)|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å|
|Authors||Famelis, N. / Rivera-Calzada, A. / Llorca, O. / Geibel, S.|
|Funding support|| Germany, Spain, 6items |
|Citation||Journal: Nature / Year: 2019|
Title: Architecture of the mycobacterial type VII secretion system.
Authors: Nikolaos Famelis / Angel Rivera-Calzada / Gianluca Degliesposti / Maria Wingender / Nicole Mietrach / J Mark Skehel / Rafael Fernandez-Leiro / Bettina Böttcher / Andreas Schlosser / Oscar ...Authors: Nikolaos Famelis / Angel Rivera-Calzada / Gianluca Degliesposti / Maria Wingender / Nicole Mietrach / J Mark Skehel / Rafael Fernandez-Leiro / Bettina Böttcher / Andreas Schlosser / Oscar Llorca / Sebastian Geibel /
Abstract: Host infection by pathogenic mycobacteria, such as Mycobacterium tuberculosis, is facilitated by virulence factors that are secreted by type VII secretion systems. A molecular understanding of the ...Host infection by pathogenic mycobacteria, such as Mycobacterium tuberculosis, is facilitated by virulence factors that are secreted by type VII secretion systems. A molecular understanding of the type VII secretion mechanism has been hampered owing to a lack of three-dimensional structures of the fully assembled secretion apparatus. Here we report the cryo-electron microscopy structure of a membrane-embedded core complex of the ESX-3/type VII secretion system from Mycobacterium smegmatis. The core of the ESX-3 secretion machine consists of four protein components-EccB3, EccC3, EccD3 and EccE3, in a 1:1:2:1 stoichiometry-which form two identical protomers. The EccC3 coupling protein comprises a flexible array of four ATPase domains, which are linked to the membrane through a stalk domain. The domain of unknown function (DUF) adjacent to the stalk is identified as an ATPase domain that is essential for secretion. EccB3 is predominantly periplasmatic, but a small segment crosses the membrane and contacts the stalk domain. This suggests that conformational changes in the stalk domain-triggered by substrate binding at the distal end of EccC3 and subsequent ATP hydrolysis in the DUF-could be coupled to substrate secretion to the periplasm. Our results reveal that the architecture of type VII secretion systems differs markedly from that of other known secretion machines, and provide a structural understanding of these systems that will be useful for the design of antimicrobial strategies that target bacterial virulence.
SummaryFull reportAbout validation report
|Structure viewer||Molecule: |
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A: ESX-3 secretion system protein EccB3
B: ESX-3 secretion system protein EccB3
Mass: 42746.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Gene: eccB3, MSMEG_0616, MSMEI_0600
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QQ39
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction|
|Component||Name: EccB3 dimeric structure from ESX-3/Type VII secretion system|
Details: The sample consists of four protein components, EccB3:EccC3:EccD3:EccE3 in a 1:1:2:1 stoichiometry Molecular weight of the complex without the amphipol micelle: 0.65 MDa
Entity ID: #1 / Source: RECOMBINANT
|Molecular weight||Value: 0.083 MDa / Experimental value: NO|
|Source (natural)||Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)|
|Source (recombinant)||Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)|
|Buffer solution||pH: 8 / Details: 30 mM Hepes pH 8.0, 150 mM NaCl|
|Specimen||Conc.: 0.3 mg/ml / Details: bound to Amphipol A8-35 / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K / Details: Blotting time: 3s Blotting force: -10|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 1600 nm / Cs: 2.7 mm|
|Specimen holder||Cryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Image recording||Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 11903 |
Details: Images acquired as 55 frames movies at a calibrated magnification of 1.0635 Angs/px
|Image processing||Details: Images were collected in counting mode|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Particle selection||Num. of particles selected: 2066007|
|Symmetry||Point symmetry: C2 (2 fold cyclic)|
|3D reconstruction||Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55342 |
Details: Particles were extracted centred at extracellular density instead than in the centre of mass in order to improve the resolution in that distal region. Extra density not corresponding to the ...Details: Particles were extracted centred at extracellular density instead than in the centre of mass in order to improve the resolution in that distal region. Extra density not corresponding to the EccB3 dimer was subtracted
Symmetry type: POINT
|Atomic model building||Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Map correlation coefficient|
Details: Two copies of the periplasmic domain of a EccB3 homology model (based on pdb 3X3M) were fitted into the density and then morphing was performed using PHENIX Real-Space Refinement.
|Atomic model building||PDB-ID: 3X3M|
Pdb chain-ID: A / Pdb chain residue range: 100-518
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