Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B1C1D1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 178.57 kDa 
• Atom Count: 11227 
• Modelled Residue Count: 1512 
• Deposited Residue Count: 1695 
• Unique protein chains: 4

6SGX

Structure of protomer 1 of the ESX-3 core complex

• PDB DOI: 10.2210/pdb6SGX/pdb
• EM Map EMD-10187: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Mycolicibacterium smegmatis MC2 155
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2019-08-05 Released: 2019-10-09 
• Deposition Author(s): Famelis, N., Rivera-Calzada, A., Llorca, O., Geibel, S.
• Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities, European Regional Development Fund, European Union, Bavarian State Ministry of Science and the Arts Funding Organisation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Architecture of the mycobacterial type VII secretion system.

Famelis, N., Rivera-Calzada, A., Degliesposti, G., Wingender, M., Mietrach, N., Skehel, J.M., Fernandez-Leiro, R., Bottcher, B., Schlosser, A., Llorca, O., Geibel, S.

(2019) Nature 576: 321-325

• PubMed: 31597161 
• DOI: 10.1038/s41586-019-1633-1
• Primary Citation of Related Structures:  
  6SGW, 6SGX, 6SGY, 6SGZ


• PubMed Abstract: 
  

Host infection by pathogenic mycobacteria, such as Mycobacterium tuberculosis, is facilitated by virulence factors that are secreted by type VII secretion systems ¹ . 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 ² , and provide a structural understanding of these systems that will be useful for the design of antimicrobial strategies that target bacterial virulence.

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Organizational Affiliation: 

Rudolf Virchow Center for Experimental Biomedicine, Julius-Maximilians-University Würzburg, Würzburg, Germany. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ESX-3 secretion system EccB3	A	79	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: eccB3, MSMEG_0616, MSMEI_0600 EC: 3.6 Membrane Entity: Yes
UniProt
Find proteins for A0QQ39 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QQ39  Go to UniProtKB:  A0QQ39

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ESX-3 secretion system protein EccD3	B, C	465	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: eccD3, snm, MSMEG_0623, MSMEI_0607 Membrane Entity: Yes
UniProt
Find proteins for A0QQ46 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QQ46  Go to UniProtKB:  A0QQ46

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ESX-3 secretion system protein EccC3	D [auth F]	401	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: eccC3, MSMEG_0617, MSMEI_0601 Membrane Entity: Yes
UniProt
Find proteins for A0QQ40 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QQ40  Go to UniProtKB:  A0QQ40

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ESX-3 secretion system protein EccE3	E [auth G]	285	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: eccE3, MSMEG_0626, MSMEI_0609 Membrane Entity: Yes
UniProt
Find proteins for A0QQ48 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QQ48  Go to UniProtKB:  A0QQ48

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-08-05 
• Released Date: 2019-10-09 
Deposition Author(s): Famelis, N., Rivera-Calzada, A., Llorca, O., Geibel, S.

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Funding Organization	Location	Grant Number
Spanish Ministry of Science, Innovation, and Universities	Spain	SAF2017-82632-P o-funded by the European Regional Development Fund
European Regional Development Fund	Spain	Y2018/BIO4747 co-funded by the Autonomous Region of Madrid
European Regional Development Fund	Spain	P2018/NMT4443 co-funded by Autonomous Region of Madrid
European Union	Spain	Horizon 2020, iNEXT (PID2907) , Grant number 653706
Bavarian State Ministry of Science and the Arts Funding Organisation	Germany	N-BM-2013-246

Revision History  

• Version 1.0: 2019-10-09
  Type: Initial release
  
• Version 1.1: 2019-10-23
  Changes: Data collection, Database references
• Version 1.2: 2019-12-25
  Changes: Database references