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- PDB-9nh2: In situ cryo-EM structure of porin III of the Legionella Dot/Icm ... -

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Basic information

Entry
Database: PDB / ID: 9nh2
TitleIn situ cryo-EM structure of porin III of the Legionella Dot/Icm T4SS machine
ComponentsOuter membrane protein beta-barrel domain-containing protein
KeywordsPROTEIN TRANSPORT / Type IVB Dot/Icm Secretion Machine
Function / homologyOuter membrane protein/outer membrane enzyme PagP, beta-barrel / Outer membrane protein beta-barrel domain-containing protein
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.05 Å
AuthorsYue, J. / Liu, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorR01AI152421 United States
CitationJournal: bioRxiv / Year: 2025
Title: structures of the Dot/Icm T4SS identify the DotA-IcmX complex as the gatekeeper for effector translocation.
Authors: Jian Yue / Samira Heydari / Donghyun Park / David Chetrit / Shoichi Tachiyama / Wangbiao Guo / Jack M Botting / Shenping Wu / Craig R Roy / Jun Liu
Abstract: The Dot/Icm machine in is one of the most versatile type IV secretion systems (T4SSs), with a remarkable capacity to translocate over 330 different effector proteins across the bacterial envelope ...The Dot/Icm machine in is one of the most versatile type IV secretion systems (T4SSs), with a remarkable capacity to translocate over 330 different effector proteins across the bacterial envelope into host cells. At least 27 Dot and Icm proteins are required for assembly and function of the system, yet the architecture and activation mechanism remain poorly understood at the molecular level. Here, we deploy cryo-electron microscopy to reveal structures of the Dot/Icm machine at near-atomic resolution. Importantly, two proteins essential for effector translocation, DotA and IcmX, form a pentameric protochannel at an inactive state. Upon activation, the DotA-IcmX protochannel undergoes extensive rearrangements to form an extended transenvelope passage capable of transporting effector proteins from the bacterial cytoplasm into host cells as revealed by cryo-electron tomography. Collectively, our findings suggest that the DotA-IcmX complex functions as the gatekeeper for effector translocation of the Dot/Icm T4SS.
History
DepositionFeb 23, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer membrane protein beta-barrel domain-containing protein
B: Outer membrane protein beta-barrel domain-containing protein
C: Outer membrane protein beta-barrel domain-containing protein
D: Outer membrane protein beta-barrel domain-containing protein
E: Outer membrane protein beta-barrel domain-containing protein
F: Outer membrane protein beta-barrel domain-containing protein
G: Outer membrane protein beta-barrel domain-containing protein
H: Outer membrane protein beta-barrel domain-containing protein
I: Outer membrane protein beta-barrel domain-containing protein
J: Outer membrane protein beta-barrel domain-containing protein
K: Outer membrane protein beta-barrel domain-containing protein
L: Outer membrane protein beta-barrel domain-containing protein
M: Outer membrane protein beta-barrel domain-containing protein
N: Outer membrane protein beta-barrel domain-containing protein
O: Outer membrane protein beta-barrel domain-containing protein
P: Outer membrane protein beta-barrel domain-containing protein


Theoretical massNumber of molelcules
Total (without water)421,83316
Polymers421,83316
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Outer membrane protein beta-barrel domain-containing protein


Mass: 26364.537 Da / Num. of mol.: 16 / Source method: isolated from a natural source
Source: (natural) Legionella pneumophila subsp. pneumophila (bacteria)
References: UniProt: Q5ZXK0
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: porin III / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Legionella pneumophila subsp. pneumophila (bacteria)
Buffer solutionpH: 6.7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI TECNAI 12
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 73 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 76409 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 21.1 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004228016
ELECTRON MICROSCOPYf_angle_d0.848738176
ELECTRON MICROSCOPYf_chiral_restr0.05694224
ELECTRON MICROSCOPYf_plane_restr0.00715008
ELECTRON MICROSCOPYf_dihedral_angle_d6.80083932

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