9NGU | pdb_00009ngu

In situ cryo-EM structure of outer membrane cap (OMC) of the Legionella Dot/Icm T4SS machine


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.96 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.1 of the entry. See complete history


Literature

In situ structures of the Legionella Dot/Icm T4SS identify the DotA-IcmX complex as the gatekeeper for effector translocation.

Yue, J.Heydari, S.Park, D.Chetrit, D.Tachiyama, S.Guo, W.Botting, J.M.Wu, S.Roy, C.R.Liu, J.

(2025) Proc Natl Acad Sci U S A 122: e2516300122-e2516300122

  • DOI: https://doi.org/10.1073/pnas.2516300122
  • Primary Citation of Related Structures:  
    9NGU, 9NGV, 9NGW, 9NGY, 9NH0, 9NH1, 9NH2

  • PubMed Abstract: 

    The Dot/Icm machine of Legionella pneumophila is among the most versatile type IV secretion systems (T4SSs), capable of translocating more than 330 distinct effector proteins across the bacterial envelope into host cells. Assembly and function of the system require at least 27 Dot and Icm proteins, yet its architecture and activation mechanism remain poorly understood at the molecular level. Here, we deploy in situ single-particle cryoelectron microscopy to determine near-atomic structures of the Dot/Icm machine and its intimate association with three distinct outer membrane porins in intact bacteria. Notably, two essential yet enigmatic components, DotA and IcmX, form a pentameric protochannel in an inactive state at the central axis of the Dot/Icm machine. Upon Dot/Icm activation with host lysate, this protochannel undergoes extensive rearrangements to generate an extended transenvelope conduit, as visualized by cryoelectron tomography (cryo-ET) and subtomogram averaging. Furthermore, a combination of cryo-ET and cryo-FIB milling of macrophages infected with L. pneumophila reveals tethering of the Dot/Icm machine to the host membrane, suggesting direct translocation of effector proteins from the bacterial cytoplasm into the host. Together, our studies identify the DotA-IcmX complex as a gatekeeper for effector translocation and provide a molecular framework for understanding the assembly and activation of the elaborate Dot/Icm T4SS.


  • Organizational Affiliation
    • Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06536.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DotD163Legionella pneumophila subsp. pneumophilaMutation(s): 0 
UniProt
Find proteins for Q5ZS45 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
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Go to UniProtKB:  Q5ZS45
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UniProt GroupQ5ZS45
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
LphA (DotK)189Legionella pneumophila subsp. pneumophilaMutation(s): 0 
UniProt
Find proteins for Q5ZYC5 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
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UniProt GroupQ5ZYC5
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Putative auto-transporter adhesin head GIN domain-containing protein320Legionella pneumophila subsp. pneumophilaMutation(s): 0 
UniProt
Find proteins for Q5ZRN3 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
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UniProt GroupQ5ZRN3
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Neurogenic locus notch protein homolog124Legionella pneumophila subsp. pneumophilaMutation(s): 0 
UniProt
Find proteins for Q5ZXA9 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
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UniProt GroupQ5ZXA9
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
IcmG (DotF)269Legionella pneumophila subsp. pneumophilaMutation(s): 0 
UniProt
Find proteins for Q5ZYC0 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
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UniProt GroupQ5ZYC0
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
IcmK (DotH)361Legionella pneumophila subsp. pneumophilaMutation(s): 0 
UniProt
Find proteins for Q5ZYC2 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane protein, OmpA family protein249Legionella pneumophila subsp. pneumophilaMutation(s): 0 
UniProt
Find proteins for Q5ZXS4 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DotC303Legionella pneumophila subsp. pneumophilaMutation(s): 0 
UniProt
Find proteins for Q5ZS44 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Secreted protein93Legionella pneumophila subsp. pneumophilaMutation(s): 0 
UniProt
Find proteins for A0AAN5PM39 (Legionella pneumophila)
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UniProt GroupA0AAN5PM39
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.96 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Office of the DirectorUnited StatesR01AI152421

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-17
    Type: Initial release
  • Version 1.1: 2025-11-12
    Changes: Data collection, Database references