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- EMDB-24773: C16 reconstruction for Outer Membrane Core Complex (OMCC) of Type... -

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Basic information

Entry
Database: EMDB / ID: EMD-24773
TitleC16 reconstruction for Outer Membrane Core Complex (OMCC) of Type IV Secretion System (T4SS) encoded by a plasmid overproducing TraV, TraK and TraB of pED208
Map dataC16 reconstruction for Outer Membrane Core Complex (OMCC) of Type IV Secretion System (T4SS) encoded by a plasmid overproducing TraV, TraK and TraB of pED208
Sample
  • Organelle or cellular component: Outer membrane core complex of T4SS encoded by a plasmid overproducing TraV, TraK and TraB of pED208
Function / homologyType IV conjugative transfer system protein TraV / Type IV conjugative transfer system lipoprotein (TraV) / Bacterial conjugation TrbI-like protein / Type IV secretion system, VirB10 / TraB / TrbI / Prokaryotic membrane lipoprotein lipid attachment site profile. / TraV / TraB
Function and homology information
Biological speciesEscherichia coli BL21(DE3) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.87 Å
AuthorsLiu X / Khara P / Baker ML / Christie PJ / Hu B
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2022
Title: Structure of a type IV secretion system core complex encoded by multi-drug resistance F plasmids.
Authors: Xiangan Liu / Pratick Khara / Matthew L Baker / Peter J Christie / Bo Hu /
Abstract: Bacterial type IV secretion systems (T4SSs) are largely responsible for the proliferation of multi-drug resistance. We solved the structure of the outer-membrane core complex (OMCC) of a T4SS encoded ...Bacterial type IV secretion systems (T4SSs) are largely responsible for the proliferation of multi-drug resistance. We solved the structure of the outer-membrane core complex (OMCC) of a T4SS encoded by a conjugative F plasmid at <3.0 Å resolution by cryoelectron microscopy. The OMCC consists of a 13-fold symmetrical outer ring complex (ORC) built from 26 copies of TraK and TraV C-terminal domains, and a 17-fold symmetrical central cone (CC) composed of 17 copies of TraB β-barrels. Domains of TraV and TraB also bind the CC and ORC substructures, establishing that these proteins undergo an intraprotein symmetry alteration to accommodate the C13:C17 symmetry mismatch. We present evidence that other pED208-encoded factors stabilize the C13:C17 architecture and define the importance of TraK, TraV and TraB domains to T4SS function. This work identifies OMCC structural motifs of proposed importance for structural transitions associated with F plasmid dissemination and F pilus biogenesis.
History
DepositionAug 27, 2021-
Header (metadata) releaseFeb 2, 2022-
Map releaseFeb 2, 2022-
UpdateFeb 15, 2023-
Current statusFeb 15, 2023Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.35
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.35
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7spk
  • Surface level: 0.35
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7spk
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24773.png

Downloads & links

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Map

FileDownload / File: emd_24773.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC16 reconstruction for Outer Membrane Core Complex (OMCC) of Type IV Secretion System (T4SS) encoded by a plasmid overproducing TraV, TraK and TraB of pED208
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 400 pix.
= 426.08 Å		1.07 Å/pix.
x 400 pix.
= 426.08 Å		1.07 Å/pix.
x 400 pix.
= 426.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0652 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35 / Movie #1: 0.35
Minimum - Maximum-0.75171745 - 1.327663
Average (Standard dev.)0.0049452926 (±0.052738365)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 426.08 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.06521.06521.0652
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z426.080426.080426.080
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.7521.3280.005

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Supplemental data

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Sample components

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Entire : Outer membrane core complex of T4SS encoded by a plasmid overprod...

EntireName: Outer membrane core complex of T4SS encoded by a plasmid overproducing TraV, TraK and TraB of pED208
Components
  • Organelle or cellular component: Outer membrane core complex of T4SS encoded by a plasmid overproducing TraV, TraK and TraB of pED208

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Supramolecule #1: Outer membrane core complex of T4SS encoded by a plasmid overprod...

SupramoleculeName: Outer membrane core complex of T4SS encoded by a plasmid overproducing TraV, TraK and TraB of pED208
type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli BL21(DE3) (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: 40.0 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

Final reconstructionApplied symmetry - Point group: C16 (16 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 21900
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC

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