9NGY | pdb_00009ngy

In situ cryo-EM structure of protochannel (DotA-IcmX) of the Legionella Dot/Icm T4SS machine


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.63 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IcmX (IcmY)A [auth AP1],
B [auth BP1],
C [auth CP1],
D [auth DP1],
E [auth EP1]
466Legionella pneumophila subsp. pneumophilaMutation(s): 0 
UniProt
Find proteins for Q5ZS30 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZS30 
Go to UniProtKB:  Q5ZS30
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZS30
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DotAF [auth FP1],
G [auth GP1],
H [auth HP1],
I [auth IP1],
J [auth JP1]
1,048Legionella pneumophila subsp. pneumophilaMutation(s): 0 
UniProt
Find proteins for Q5ZS33 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZS33 
Go to UniProtKB:  Q5ZS33
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZS33
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
IcmE (DotG)K [auth KP1],
L [auth LP1],
M [auth MP1],
N [auth NP1],
O [auth OP1]
1,048Legionella pneumophila subsp. pneumophilaMutation(s): 0 
UniProt
Find proteins for Q5ZYC1 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZYC1 
Go to UniProtKB:  Q5ZYC1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZYC1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.63 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