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- EMDB-70323: Cryo-EM Structure of the Legionella pneumophila delta dis2 OMC -

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Basic information

Entry
Database: EMDB / ID: EMD-70323
TitleCryo-EM Structure of the Legionella pneumophila delta dis2 OMC
Map dataPrimary EM map
Sample
  • Complex: Outer membrane complex of the Dot/Icm T4SS purified from a Dis3 deletion strain of Legionella pneumophila
KeywordsT4SS / outer membrane / translocon / MEMBRANE PROTEIN
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.1 Å
AuthorsRoberts JR
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Library of Medicine (NIH/NLM)S10OD030275 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI118932 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)F32AI150027 United States
National Science Foundation (NSF, United States)2241144 United States
CitationJournal: J Mol Biol / Year: 2025
Title: The Legionella pneumophila Dot/Icm Type IV Secretion System is Structurally and Functionally Resilient in Absence of Species-specific Proteins Dis2 and Dis3.
Authors: Jacquelyn R Roberts / Arwen E Frick-Cheng / Henry J Styron / Clarissa L Durie / Louise Chang / Melanie D Ohi /
Abstract: Legionella pneumophila is a pathogenic Gram-negative bacterium that causes Legionnaires' disease. The main virulence factor of L. pneumophila is the Dot/Icm Type IV Secretion System (T4SS), which ...Legionella pneumophila is a pathogenic Gram-negative bacterium that causes Legionnaires' disease. The main virulence factor of L. pneumophila is the Dot/Icm Type IV Secretion System (T4SS), which translocates effector proteins into the cytoplasm of the host cell, allowing the bacterium to establish a replicative niche. The outer membrane core complex (OMCC), the T4SS machinery localized between the inner and outer membranes, is composed of at least nine proteins organized into various sub-complexes that include the dome, outer membrane cap (OMC), periplasmic ring (PR), and stalk. In this study we describe how two uncharacterized Dot/Icm T4SS components, Dis2 and Dis3, contribute to the structure of the T4SS, the ability of the T4SS to translocate effectors, and the pathogenicity of L. pneumophila. Using cryo-electron microscopy we show that OMCCs purified from a Δdis2 strain are only missing the density for Dis2, while OMCCs purified from the Δdis3 strain lack densities for Dis3 and DotF in the OMC. Despite missing these proteins, the OMC and PR of both mutant OMCCs remain structurally stable. Strains lacking dis2 and or dis3 efficiently replicate in human macrophages; however, they have subtle differences in translocation efficiency for four tested substrates. Combined these data indicate that Dis2 or Dis3 are not required for the stability or global organization of the OMCC, but each protein may contribute to the efficient translocation of specific effectors.
History
DepositionApr 24, 2025-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70323.png

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Map

FileDownload / File: emd_70323.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary EM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 600 pix.
= 648. Å		1.08 Å/pix.
x 600 pix.
= 648. Å		1.08 Å/pix.
x 600 pix.
= 648. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.25093275 - 0.54919946
Average (Standard dev.)0.0009182359 (±0.015899142)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 648.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map B

Fileemd_70323_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_70323_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Outer membrane complex of the Dot/Icm T4SS purified from a Dis3 d...

EntireName: Outer membrane complex of the Dot/Icm T4SS purified from a Dis3 deletion strain of Legionella pneumophila
Components
  • Complex: Outer membrane complex of the Dot/Icm T4SS purified from a Dis3 deletion strain of Legionella pneumophila

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Supramolecule #1: Outer membrane complex of the Dot/Icm T4SS purified from a Dis3 d...

SupramoleculeName: Outer membrane complex of the Dot/Icm T4SS purified from a Dis3 deletion strain of Legionella pneumophila
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 20 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C13 (13 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9017
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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