6SGZ

Structure of protomer 2 of the ESX-3 core complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

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

  • 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 ...

    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.


    Organizational Affiliation

    Rudolf Virchow Center for Experimental Biomedicine, Julius-Maximilians-University Würzburg, Würzburg, Germany. sebastian.geibel@uni-wuerzburg.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ESX-3 secretion system protein EccD3A [auth E], B [auth H]467Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: eccD3snmMSMEG_0623MSMEI_0607
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Type VII Secretion Systems
Protein: 
Mycobacterial secretion system, ESX-3 core complex
Find proteins for A0QQ46 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QQ46 
Go to UniProtKB:  A0QQ46
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ESX-3 secretion system ATPase EccB3C [auth I]59Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: eccB3MSMEG_0616MSMEI_0600
EC: 3.6
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Type VII Secretion Systems
Protein: 
Mycobacterial secretion system, ESX-3 core complex
Find proteins for A0QQ39 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QQ39 
Go to UniProtKB:  A0QQ39
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ESX-3 secretion system protein EccC3D [auth J]343Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: eccC3MSMEG_0617MSMEI_0601
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
ESX-3 secretion system protein EccE3E [auth D]286Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: eccE3MSMEG_0626MSMEI_0609
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Type VII Secretion Systems
Protein: 
Mycobacterial secretion system, ESX-3 core complex
Find proteins for A0QQ48 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QQ48 
Go to UniProtKB:  A0QQ48
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainSAF2017-82632-P o-funded by the European Regional Development Fund
European Regional Development FundSpainY2018/BIO4747 co-funded by the Autonomous Region of Madrid
European Regional Development FundSpainP2018/NMT4443 co-funded by Autonomous Region of Madrid
European UnionSpainHorizon 2020, iNEXT (PID2907) , Grant number 653706
Bavarian State Ministry of Science and the Arts Funding OrganisationGermanyN-BM-2013-246

Revision History  (Full details and data files)

  • 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