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- EMDB-13859: L. pneumophila Type IV Coupling Complex (T4CC) computed from a sa... -

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Basic information

Entry
Database: EMDB / ID: EMD-13859
TitleL. pneumophila Type IV Coupling Complex (T4CC) computed from a sample where dotY/Z genes were deleted (referred to as T4CCdeltaDotYZ at 15A)
Map data
SampleDotLMN_IcmSW
Function / homologyTraD/TraG, TraM recognition site / TraM recognition site of TraD and TraG / HNH nucleases / HNH nuclease / P-loop containing nucleoside triphosphate hydrolase / integral component of membrane / IcmJ (DotN) / IcmO (DotL) / IcmP (DotM)
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 15 Å
AuthorsMace K / Meir A / Lukoyanova N / Waksman G
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)321630European Union
CitationJournal: Mol Microbiol / Year: 2021
Title: Proteins DotY and DotZ modulate the dynamics and localization of the type IVB coupling complex of Legionella pneumophila.
Authors: Kevin Macé / Amit Meir / Natalya Lukoyanova / Luying Liu / David Chetrit / Manuela K Hospenthal / Craig R Roy / Gabriel Waksman /
Abstract: Legionella pneumophila is an opportunistic pathogen infecting alveolar macrophages and protozoa species. Legionella utilizes a Type IV Secretion System (T4SS) to translocate over 300 effector ...Legionella pneumophila is an opportunistic pathogen infecting alveolar macrophages and protozoa species. Legionella utilizes a Type IV Secretion System (T4SS) to translocate over 300 effector proteins into its host cell. In a recent study, we have isolated and solved the cryo-EM structure of the Type IV Coupling Complex (T4CC), a large cytoplasmic determinant associated with the inner membrane that recruits effector proteins for delivery to the T4SS for translocation. The T4CC is composed of a DotLMNYZ hetero-pentameric core from which the flexible IcmSW module flexibly protrudes. The DotY and DotZ proteins were newly reported members of this complex and their role remained elusive. In this study, we observed the effect of deleting DotY and DotZ on T4CC stability and localization. Furthermore, we found these two proteins are co-dependent, whereby the deletion of DotY resulted in DotZ absence from the coupling complex, and vice versa. Additional cryo-EM data analysis revealed the dynamic movement of the IcmSW module is modified by the DotY/Z proteins. We therefore determined the likely function of DotY and DotZ and revealed their importance on T4CC function.
History
DepositionNov 8, 2021-
Header (metadata) releaseDec 1, 2021-
Map releaseDec 1, 2021-
UpdateDec 22, 2021-
Current statusDec 22, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_13859.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 300 pix.
= 313.5 Å
1.05 Å/pix.
x 300 pix.
= 313.5 Å
1.05 Å/pix.
x 300 pix.
= 313.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.3
Minimum - Maximum-0.3582014 - 1.191663
Average (Standard dev.)0.0034178917 (±0.03092653)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 313.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0451.0451.045
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z313.500313.500313.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.3581.1920.003

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Supplemental data

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Sample components

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Entire DotLMN_IcmSW

EntireName: DotLMN_IcmSW / Details: Heterogeneity from DotLMNYZ_IcmSW WT / Number of Components: 1

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Component #1: protein, DotLMN_IcmSW

ProteinName: DotLMN_IcmSW
Details: Heterogeneity from DotLMNYZ_IcmSW WTHomogeneity and heterogeneity
Recombinant expression: No
SourceSpecies: Legionella pneumophila (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 8
VitrificationCryogen Name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 54 e/Å2 / Illumination Mode: FLOOD BEAM
LensImaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of Projections: 50210
3D reconstructionResolution: 15 Å / Resolution Method: FSC 0.143 CUT-OFF

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