6X6S

Cryo-EM Structure of the Helicobacter pylori OMC

  • Classification: PROTEIN TRANSPORT
  • Organism(s): Helicobacter pylori
  • Mutation(s): No 

  • Deposited: 2020-05-29 Released: 2020-10-07 
  • Deposition Author(s): Sheedlo, M.J., Chung, J.M., Sawhney, N., Durie, C.L., Cover, T.L., Ohi, M.D., Lacy, D.B.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/Office of the Director, Other government

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 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

Cryo-EM reveals species-specific components within the Helicobacter pylori Cag type IV secretion system core complex.

Sheedlo, M.J.Chung, J.M.Sawhney, N.Durie, C.L.Cover, T.L.Ohi, M.D.Lacy, D.B.

(2020) Elife 9

  • DOI: https://doi.org/10.7554/eLife.59495
  • Primary Citation of Related Structures:  
    6X6J, 6X6K, 6X6L, 6X6S

  • PubMed Abstract: 

    The pathogenesis of Helicobacter pylori -associated gastric cancer is dependent on delivery of CagA into host cells through a type IV secretion system (T4SS). The H. pylori Cag T4SS includes a large membrane-spanning core complex containing five proteins, organized into an outer membrane cap (OMC), a periplasmic ring (PR) and a stalk. Here, we report cryo-EM reconstructions of a core complex lacking Cag3 and an improved map of the wild-type complex. We define the structures of two unique species-specific components (Cag3 and CagM) and show that Cag3 is structurally similar to CagT. Unexpectedly, components of the OMC are organized in a 1:1:2:2:5 molar ratio (CagY:CagX:CagT:CagM:Cag3). CagX and CagY are components of both the OMC and the PR and bridge the symmetry mismatch between these regions. These results reveal that assembly of the H. pylori T4SS core complex is dependent on incorporation of interwoven species-specific components.


  • Organizational Affiliation

    Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Type IV secretion system apparatus protein Cag3481Helicobacter pyloriMutation(s): 0 
UniProt
Find proteins for A0A2J9KJK3 (Helicobacter pylori)
Explore A0A2J9KJK3 
Go to UniProtKB:  A0A2J9KJK3
Entity Groups  
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UniProt GroupA0A2J9KJK3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Type IV secretion system apparatus protein CagM376Helicobacter pyloriMutation(s): 0 
UniProt
Find proteins for A0A2J9KJL4 (Helicobacter pylori)
Explore A0A2J9KJL4 
Go to UniProtKB:  A0A2J9KJL4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2J9KJL4
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Type IV secretion system apparatus protein CagT280Helicobacter pyloriMutation(s): 0 
UniProt
Find proteins for Q6VRP0 (Helicobacter pylori)
Explore Q6VRP0 
Go to UniProtKB:  Q6VRP0
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UniProt GroupQ6VRP0
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown protein fragment160Helicobacter pyloriMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Type IV secretion system apparatus protein CagX522Helicobacter pyloriMutation(s): 0 
UniProt
Find proteins for A0A2J9KJM4 (Helicobacter pylori)
Explore A0A2J9KJM4 
Go to UniProtKB:  A0A2J9KJM4
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UniProt GroupA0A2J9KJM4
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  • Reference Sequence
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cag pathogenicity island protein (Cag7)1,927Helicobacter pyloriMutation(s): 0 
UniProt
Find proteins for O25262 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore O25262 
Go to UniProtKB:  O25262
Entity Groups  
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UniProt GroupO25262
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI118932
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA116087
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI039657
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM103310
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United States2T32DK007673
National Institutes of Health/Office of the DirectorUnited StatesS10OD020011
Other governmentUnited States1I01BX004447

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-07
    Type: Initial release
  • Version 1.1: 2021-04-14
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references