9NH0 | pdb_00009nh0

In situ cryo-EM structure of PR and DotA-IcmX of the Legionella Dot/Icm T4SS machine at C1 symmetry


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.63 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
unknown peptide E16Legionella pneumophila subsp. pneumophilaMutation(s): 0 
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
unknown peptide F9Legionella pneumophila subsp. pneumophilaMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
unknown peptide G16Legionella pneumophila subsp. pneumophilaMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
unknown peptide H5Legionella pneumophila subsp. pneumophilaMutation(s): 0 
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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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Go to UniProtKB:  Q5ZYC0
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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
IcmE (DotG)1,048Legionella pneumophila subsp. pneumophilaMutation(s): 0 
UniProt
Find proteins for Q5ZYC1 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
IcmX (IcmY)AE [auth Fa],
WD [auth Ew],
XD [auth Ex],
YD [auth Ey],
ZD [auth Ez]
466Legionella pneumophila subsp. pneumophilaMutation(s): 0 
UniProt
Find proteins for Q5ZS30 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DotABE [auth Fb],
CE [auth Fc],
DE [auth Fd],
EE [auth Fe],
FE [auth Ff]
1,048Legionella pneumophila subsp. pneumophilaMutation(s): 0 
UniProt
Find proteins for Q5ZS33 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
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UniProt GroupQ5ZS33
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.63 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