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- EMDB-13858: L. pneumophila Type IV Coupling Complex (T4CC) computed from WT p... -

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Basic information

Entry
Database: EMDB / ID: EMD-13858
TitleL. pneumophila Type IV Coupling Complex (T4CC) computed from WT particles where DotY/Z is missing (referred to as T4CCWTminusYZ at 6.3A)
Map dataT4CCWTminusYZ at 6.3A sharpened
Sample
  • Complex: DotLMN_IcmSW
KeywordsType IV Coupling Complex / T4CC / Type IV Secretion System / T4SS / Membrane protein complex / Membrane complex / DotY / DotZ / DotL / dotM / dotN / IcmSW / Legionella / MEMBRANE PROTEIN / delta DotY/Z
Function / homology
Function and homology information


protein transport / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
: / TraD/TraG, TraM recognition site / TraM recognition site of TraD and TraG / : / : / HNH nucleases / HNH nuclease / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Type 4 apparatus protein DotN / Type 4 coupling protein DotL / Type 4 apparatus protein DotM
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.3 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: 2022
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 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13858.png

Downloads & links

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Map

FileDownload / File: emd_13858.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationT4CCWTminusYZ at 6.3A sharpened
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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0 / Movie #1: 4
Minimum - Maximum-21.310500999999999 - 31.445297
Average (Standard dev.)-0.00078331004 (±0.45057166)
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
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-21.31131.445-0.001

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Supplemental data

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Sample components

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Entire : DotLMN_IcmSW

EntireName: DotLMN_IcmSW
Components
  • Complex: DotLMN_IcmSW

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Supramolecule #1: DotLMN_IcmSW

SupramoleculeName: DotLMN_IcmSW / type: complex / ID: 1 / Parent: 0 / Details: Heterogeneity from DotLMNYZ_IcmSW WT
Source (natural)Organism: Legionella pneumophila (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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

10350

Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 166260
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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