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- EMDB-13231: Outer-membrane core complex C1 map -

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Basic information

Entry
Database: EMDB / ID: EMD-13231
TitleOuter-membrane core complex C1 map
Map data
SampleOuter-membrane core complex C1 map
Function / homologyType IV conjugative transfer system protein TraV / Type IV conjugative transfer system lipoprotein (TraV) / Type IV conjugative transfer system lipoprotein TraV
Function and homology information
Biological speciesSalmonella enterica (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.7 Å
AuthorsAmin H / Ilangovan A / Costa TRD
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust215164/Z/18/Z United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: Architecture of the outer-membrane core complex from a conjugative type IV secretion system.
Authors: Himani Amin / Aravindan Ilangovan / Tiago R D Costa /
Abstract: Conjugation is one of the most important processes that bacteria utilize to spread antibiotic resistance genes among bacterial populations. Interbacterial DNA transfer requires a large double ...Conjugation is one of the most important processes that bacteria utilize to spread antibiotic resistance genes among bacterial populations. Interbacterial DNA transfer requires a large double membrane-spanning nanomachine called the type 4 secretion system (T4SS) made up of the inner-membrane complex (IMC), the outer-membrane core complex (OMCC) and the conjugative pilus. The iconic F plasmid-encoded T4SS has been central in understanding conjugation for several decades, however atomic details of its structure are not known. Here, we report the structure of a complete conjugative OMCC encoded by the pED208 plasmid from E. coli, solved by cryo-electron microscopy at 3.3 Å resolution. This 2.1 MDa complex has a unique arrangement with two radial concentric rings, each having a different symmetry eventually contributing to remarkable differences in protein stoichiometry and flexibility in comparison to other OMCCs. Our structure suggests that F-OMCC is a highly dynamic complex, with implications for pilus extension and retraction during conjugation.
History
DepositionJul 18, 2021-
Header (metadata) releaseDec 1, 2021-
Map releaseDec 1, 2021-
UpdateDec 8, 2021-
Current statusDec 8, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.34
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.34
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_13231.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 480 pix.
= 528. Å
1.1 Å/pix.
x 480 pix.
= 528. Å
1.1 Å/pix.
x 480 pix.
= 528. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.34 / Movie #1: 0.34
Minimum - Maximum-0.5948993 - 1.4263247
Average (Standard dev.)0.0010740067 (±0.047353927)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 528.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z528.000528.000528.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.5951.4260.001

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Supplemental data

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Sample components

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Entire Outer-membrane core complex C1 map

EntireName: Outer-membrane core complex C1 map / Number of Components: 1

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Component #1: protein, Outer-membrane core complex C1 map

ProteinName: Outer-membrane core complex C1 map / Recombinant expression: No
SourceSpecies: Salmonella enterica (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 7.5
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: 1.3 e/Å2 / Illumination Mode: SPOT SCAN
LensImaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 95177
3D reconstructionResolution: 5.7 Å / Resolution Method: FSC 0.143 CUT-OFF

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