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- EMDB-12963: Structure of the outer-membrane core complex (outer ring) from a ... -

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Basic information

Entry
Database: EMDB / ID: EMD-12963
TitleStructure of the outer-membrane core complex (outer ring) from a conjugative type IV secretion system
Map dataThe structure of the outer-membrane core complex (outer ring) from a conjugative type IV secretion system
Sample
  • Complex: Outer-membrane core complex (outer ring)
    • Protein or peptide: Type IV conjugative transfer system lipoprotein TraV
    • Protein or peptide: TraB
  • Protein or peptide: Type-F conjugative transfer system secretin TraK
KeywordsType IV secretion system / F plasmid / outer-membrane core complex / conjugation / MEMBRANE PROTEIN
Function / homology
Function and homology information


Pilus assembly TraK / Type-F conjugative transfer system secretin TraK / : / TraK N-terminal domain / TraK C-terminal domain / Type IV conjugative transfer system protein TraV / Type IV conjugative transfer system lipoprotein (TraV) / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Type-F conjugative transfer system secretin TraK / Type IV conjugative transfer system lipoprotein TraV
Similarity search - Component
Biological speciesSalmonella enterica (bacteria) / Salmonella enterica subsp. salamae serovar 58:l,z13,z28:z6 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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
DepositionMay 18, 2021-
Header (metadata) releaseDec 8, 2021-
Map releaseDec 8, 2021-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing 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
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  • Surface view colored by cylindrical radius
  • Surface level: 0.34
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7oko
  • Surface level: 0.34
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7oko
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12963.png

Downloads & links

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Map

FileDownload / File: emd_12963.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe structure of the outer-membrane core complex (outer ring) from a conjugative type IV secretion system
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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.34 / Movie #1: 0.34
Minimum - Maximum-0.6226667 - 1.688174
Average (Standard dev.)0.0014677589 (±0.049790714)
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-0.6231.6880.001

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Supplemental data

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Sample components

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Entire : Outer-membrane core complex (outer ring)

EntireName: Outer-membrane core complex (outer ring)
Components
  • Complex: Outer-membrane core complex (outer ring)
    • Protein or peptide: Type IV conjugative transfer system lipoprotein TraV
    • Protein or peptide: TraB
  • Protein or peptide: Type-F conjugative transfer system secretin TraK

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Supramolecule #1: Outer-membrane core complex (outer ring)

SupramoleculeName: Outer-membrane core complex (outer ring) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Salmonella enterica (bacteria)

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Macromolecule #1: Type IV conjugative transfer system lipoprotein TraV

MacromoleculeName: Type IV conjugative transfer system lipoprotein TraV / type: protein_or_peptide / ID: 1 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica (bacteria)
Molecular weightTheoretical: 20.92865 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKITLLLAG SALLLSGCAG VKSSFDCDAT TSDTCMTMTK ANQLARDKAA KQAGKPAAGG LPSLVNLPAT SAVEVPSASR SAVTPPSGT RTVSTTPPVS AGTSAGVNTN TTTSTLTPRP VAGTPVTTTP SSVAYRPVVS VVTPTPSCQN VRCDNPGTVH P QRSRDQIA ...String:
MKKITLLLAG SALLLSGCAG VKSSFDCDAT TSDTCMTMTK ANQLARDKAA KQAGKPAAGG LPSLVNLPAT SAVEVPSASR SAVTPPSGT RTVSTTPPVS AGTSAGVNTN TTTSTLTPRP VAGTPVTTTP SSVAYRPVVS VVTPTPSCQN VRCDNPGTVH P QRSRDQIA TVWIAPWVDS DNAFHQPGRV SFVVSPADWV LPARVN

UniProtKB: Type IV conjugative transfer system lipoprotein TraV

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Macromolecule #2: TraB

MacromoleculeName: TraB / type: protein_or_peptide / ID: 2 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica (bacteria)
Molecular weightTheoretical: 1.128233 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PGMMDSQEFS

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Macromolecule #3: Type-F conjugative transfer system secretin TraK

MacromoleculeName: Type-F conjugative transfer system secretin TraK / type: protein_or_peptide / ID: 3 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. salamae serovar 58:l,z13,z28:z6 (bacteria)
Molecular weightTheoretical: 23.312551 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AQSPATISLP QGGQFRLSIS NTDPNMIFIP GDKVTAITAP GGMLADKRLT TAGGVLFTSV ATRTFTIFVE TALGQTFSVV ATPVKGEGR VYRLMSAEPP SRPETRKWET AQAYEKLLIS LNRAVLTGDI PDGYGEVKPL SDGIRLPGGF SVTPLKAWAG D QLRADRYE ...String:
AQSPATISLP QGGQFRLSIS NTDPNMIFIP GDKVTAITAP GGMLADKRLT TAGGVLFTSV ATRTFTIFVE TALGQTFSVV ATPVKGEGR VYRLMSAEPP SRPETRKWET AQAYEKLLIS LNRAVLTGDI PDGYGEVKPL SDGIRLPGGF SVTPLKAWAG D QLRADRYE LRNANTWGVA LREQDFWKPG VRAVMFDNNA QTLMGGGRMT VTVIRGNG

UniProtKB: Type-F conjugative transfer system secretin TraK

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 298235
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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