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- EMDB-12962: Structure of the outer-membrane core complex (inner ring) from a ... -

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Basic information

Entry
Database: EMDB / ID: EMD-12962
TitleStructure of the outer-membrane core complex (inner ring) from a conjugative type IV secretion system
Map dataStructure of the outer-membrane core complex (inner ring) from a conjugative type IV secretion system
Sample
  • Complex: Outer-membrane core complex (inner ring)
    • Protein or peptide: TraB
    • Protein or peptide: Type IV conjugative transfer system lipoprotein TraV
KeywordsType IV secretion system / F plasmid / outer-membrane core complex / conjugation / MEMBRANE PROTEIN
Function / homologyType IV conjugative transfer system protein TraV / Type IV conjugative transfer system lipoprotein (TraV) / Prokaryotic membrane lipoprotein lipid attachment site profile. / Type IV conjugative transfer system lipoprotein TraV
Function and homology information
Biological speciesSalmonella enterica (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.34 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 1, 2021-
Map releaseDec 1, 2021-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.265
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.265
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7okn
  • Surface level: 0.265
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7okn
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12962.png

Downloads & links

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Map

FileDownload / File: emd_12962.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the outer-membrane core complex (inner 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: 0.265 / Movie #1: 0.265
Minimum - Maximum-1.0604223 - 1.7782656
Average (Standard dev.)0.0010338143 (±0.041397203)
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-1.0601.7780.001

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Supplemental data

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Sample components

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Entire : Outer-membrane core complex (inner ring)

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

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

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

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Macromolecule #1: TraB

MacromoleculeName: TraB / type: protein_or_peptide / ID: 1 / Details: TraB / Number of copies: 17 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica (bacteria)
Molecular weightTheoretical: 48.802102 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MANVNKVVRR RQVALLIALV LGIGAGGAGT WMVSEMNLKK APPAKAPKGE PAPDMTGVVN QSFDNKVQRS AIAEAQRLNK ETQTEIKKL RTEMGLVSRD LKGSQDRIRE LEDQNQLLQT QLEAGKNFDS LSAEPLPGAL ASQGKPAPAG NVPPPTSFWP A GGGQAPAA ...String:
MANVNKVVRR RQVALLIALV LGIGAGGAGT WMVSEMNLKK APPAKAPKGE PAPDMTGVVN QSFDNKVQRS AIAEAQRLNK ETQTEIKKL RTEMGLVSRD LKGSQDRIRE LEDQNQLLQT QLEAGKNFDS LSAEPLPGAL ASQGKPAPAG NVPPPTSFWP A GGGQAPAA PVMTPIQRPG MMDSQEFSLP DTGPKKPRFP WISSGSFVEA IVVEGADANA SVTGDKNTAP MQLRLTGKVQ MP NDEEFDL TGCFVTLEAW GDVSSERAIV RSRSISCKLG DDDIDQKIAG HVSFMGKNGI KGEVVMRNGQ ILLYAGGAGF LDG IGKGIE KASSTTVGVG ATASMSAADI GQAGLGGGVS SAAKTLSDYY IKRAEQYHPV IPIGAGNEVT LVFQDGFQLE TLEE ARAKA AARKKQNQPS ASSTPAAMPG NTPDMLKQLQ DFRVGDTVDP ATGQVVTQWS HPQFEK

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Macromolecule #2: Type IV conjugative transfer system lipoprotein TraV

MacromoleculeName: Type IV conjugative transfer system lipoprotein TraV / type: protein_or_peptide / ID: 2 / Details: TraV / Number of copies: 17 / 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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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: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 74956
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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