7MUC | pdb_00007muc

Legionella pneumophila Dot/Icm T4SS C1 Reconstruction

  • Classification: TRANSLOCASE
  • Organism(s): Legionella pneumophila
  • Mutation(s): No 

  • Deposited: 2021-05-14 Released: 2021-10-06 
  • Deposition Author(s): Sheedlo, M.J., Durie, C.L., Swanson, M., Lacy, D.B., Ohi, M.D.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Other government

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Cryo-EM reveals new species-specific proteins and symmetry elements in the Legionella pneumophila Dot/Icm T4SS.

Sheedlo, M.J.Durie, C.L.Chung, J.M.Chang, L.Roberts, J.Swanson, M.Lacy, D.B.Ohi, M.D.

(2021) Elife 10

  • DOI: https://doi.org/10.7554/eLife.70427
  • Primary Citation Related Structures: 
    7MUC, 7MUD, 7MUE, 7MUQ, 7MUS, 7MUV, 7MUW, 7MUY

  • PubMed Abstract: 

    Legionella pneumophila is an opportunistic pathogen that causes the potentially fatal pneumonia known as Legionnaires' disease. The pathology associated with infection depends on bacterial delivery of effector proteins into the host via the membrane spanning Dot/Icm type IV secretion system (T4SS). We have determined sub-3.0 Å resolution maps of the Dot/Icm T4SS core complex by single particle cryo-EM. The high-resolution structural analysis has allowed us to identify proteins encoded outside the Dot/Icm genetic locus that contribute to the core T4SS structure. We can also now define two distinct areas of symmetry mismatch, one that connects the C18 periplasmic ring (PR) and the C13 outer membrane cap (OMC) and one that connects the C13 OMC with a 16-fold symmetric dome. Unexpectedly, the connection between the PR and OMC is DotH, with five copies sandwiched between the OMC and PR to accommodate the symmetry mismatch. Finally, we observe multiple conformations in the reconstructions that indicate flexibility within the structure.


  • Organizational Affiliation
    • Department of Pharmacology, University of Minnesota, Minneapolis, United States.

Macromolecule Content 

  • Total Structure Weight: 5,836.69 kDa 
  • Atom Count: 180,380 
  • Modeled Residue Count: 23,455 
  • Deposited Residue Count: 54,325 
  • Unique protein chains: 11

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DotC303Legionella pneumophilaMutation(s): 0 
UniProt
Find proteins for O52184 (Legionella pneumophila)
Explore O52184 
Go to UniProtKB:  O52184
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UniProt GroupO52184
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DotD163Legionella pneumophilaMutation(s): 0 
UniProt
Find proteins for O52183 (Legionella pneumophila)
Explore O52183 
Go to UniProtKB:  O52183
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UniProt GroupO52183
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
DotF269Legionella pneumophilaMutation(s): 0 
UniProt
Find proteins for O54615 (Legionella pneumophila)
Explore O54615 
Go to UniProtKB:  O54615
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UniProt GroupO54615
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
IcmE protein1,048Legionella pneumophilaMutation(s): 0 
UniProt
Find proteins for O53087 (Legionella pneumophila)
Explore O53087 
Go to UniProtKB:  O53087
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UniProt GroupO53087
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Inner membrane lipoprotein YiaD189Legionella pneumophilaMutation(s): 0 
UniProt
Find proteins for O53086 (Legionella pneumophila)
Explore O53086 
Go to UniProtKB:  O53086
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UniProt GroupO53086
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Outer membrane protein, OmpA family protein249Legionella pneumophilaMutation(s): 0 
UniProt
Find proteins for Q5ZXS4 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZXS4 
Go to UniProtKB:  Q5ZXS4
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UniProt GroupQ5ZXS4
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01AI118932
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesF32 AI150027-01
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States2T32DK007673
Other governmentUnited StatesS10OD020011

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-06
    Type: Initial release
  • Version 1.1: 2022-04-20
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Structure summary