7OSL | pdb_00007osl

Cryo-EM structure of nonameric EPEC SctV-C

• PDB DOI: https://doi.org/10.2210/pdb7OSL/pdb
• EM Map EMD-13054: EMDB EMDataResource

• Classification: PROTEIN TRANSPORT
• Organism(s): Escherichia coli O127:H6 str. E2348/69
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2021-06-09 Released: 2021-09-29 
• Deposition Author(s): Fahrenkamp, D., Wald, J., Yuan, B., Marlovits, T.C.
• Funding Organization(s): Austrian Science Fund

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural Dynamics of the Functional Nonameric Type III Translocase Export Gate.

Yuan, B., Portaliou, A.G., Parakra, R., Smit, J.H., Wald, J., Li, Y., Srinivasu, B., Loos, M.S., Dhupar, H.S., Fahrenkamp, D., Kalodimos, C.G., Duong van Hoa, F., Cordes, T., Karamanou, S., Marlovits, T.C., Economou, A.

(2021) J Mol Biology 433: 167188-167188

• PubMed: 34454944 
• DOI: https://doi.org/10.1016/j.jmb.2021.167188
• Primary Citation of Related Structures:  
  7OSL


• PubMed Abstract: 
  

  Type III protein secretion is widespread in Gram-negative pathogens. It comprises the injectisome with a surface-exposed needle and an inner membrane translocase. The translocase contains the SctRSTU export channel enveloped by the export gate subunit SctV that binds chaperone/exported clients and forms a putative ante-chamber. We probed the assembly, function, structure and dynamics of SctV from enteropathogenic E. coli (EPEC). In both EPEC and E. coli lab strains, SctV forms peripheral oligomeric clusters that are detergent-extracted as homo-nonamers. Membrane-embedded SctV ₉ is necessary and sufficient to act as a receptor for different chaperone/exported protein pairs with distinct C-domain binding sites that are essential for secretion. Negative staining electron microscopy revealed that peptidisc-reconstituted His-SctV ₉ forms a tripartite particle of ∼22 nm with a N-terminal domain connected by a short linker to a C-domain ring structure with a ∼5 nm-wide inner opening. The isolated C-domain ring was resolved with cryo-EM at 3.1 Å and structurally compared to other SctV homologues. Its four sub-domains undergo a three-stage "pinching" motion. Hydrogen-deuterium exchange mass spectrometry revealed this to involve dynamic and rigid hinges and a hyper-flexible sub-domain that flips out of the ring periphery and binds chaperones on and between adjacent protomers. These motions are coincident with local conformational changes at the pore surface and ring entry mouth that may also be modulated by the ATPase inner stalk. We propose that the intrinsic dynamics of the SctV protomer are modulated by chaperones and the ATPase and could affect allosterically the other subunits of the nonameric ring during secretion.

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Organizational Affiliation: 
• KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium; Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607 Hamburg, Germany; University Medical Center Hamburg-Eppendorf (UKE), Institute for Structural and Systems Biology, Notkestrasse 85, D-22607 Hamburg, Germany; German Electron Synchrotron Centre (DESY), Notkestrasse 85, D-22607 Hamburg, Germany. Electronic address: [e-mail].
KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium. Electronic address: [e-mail].
KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium. Electronic address: [e-mail].
KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium; Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands. Electronic address: [e-mail].
Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607 Hamburg, Germany; University Medical Center Hamburg-Eppendorf (UKE), Institute for Structural and Systems Biology, Notkestrasse 85, D-22607 Hamburg, Germany; German Electron Synchrotron Centre (DESY), Notkestrasse 85, D-22607 Hamburg, Germany. Electronic address: [e-mail].
Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands. Electronic address: [e-mail].
KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium. Electronic address: [e-mail].
KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium.
Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, Canada.
Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607 Hamburg, Germany; University Medical Center Hamburg-Eppendorf (UKE), Institute for Structural and Systems Biology, Notkestrasse 85, D-22607 Hamburg, Germany; German Electron Synchrotron Centre (DESY), Notkestrasse 85, D-22607 Hamburg, Germany. Electronic address: [e-mail].
Department of Structural Biology, St. Jude Children's Research Hospital, 263 Danny Thomas Place, Memphis, TN 38105, United States. Electronic address: [e-mail].
Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, Canada. Electronic address: [e-mail].
Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands; Physical and Synthetic Biology, Faculty of Biology, Ludwig Maximilians-Universität München, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany. Electronic address: [e-mail].
KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium. Electronic address: [e-mail].
Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607 Hamburg, Germany; University Medical Center Hamburg-Eppendorf (UKE), Institute for Structural and Systems Biology, Notkestrasse 85, D-22607 Hamburg, Germany; German Electron Synchrotron Centre (DESY), Notkestrasse 85, D-22607 Hamburg, Germany. Electronic address: [e-mail].
KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C9  (Explore in 3D)
Global Stoichiometry: Homo 9-mer - A9 

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

Biological Assembly Evidence: light scattering, mass spectrometry

Macromolecule Content 

• Total Structure Weight: 341.57 kDa 
• Atom Count: 23,660 
• Modeled Residue Count: 2,935 
• Deposited Residue Count: 2,979 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Translocator EscV	A, B, C, D, E, F, G, H, I	331	Escherichia coli O127:H6 str. E2348/69	Mutation(s): 0  Gene Names: escV, E2348C_3949
UniProt
Find proteins for B7UMA7 (Escherichia coli O127:H6 (strain E2348/69 / EPEC)) Explore B7UMA7  Go to UniProtKB:  B7UMA7

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-09-29 
Deposition Author(s): Fahrenkamp, D., Wald, J., Yuan, B., Marlovits, T.C.

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Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	I 2408-B22

Revision History  

• Version 1.0: 2021-09-29
  Type: Initial release
  
• Version 1.1: 2024-07-17
  Changes: Data collection