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- EMDB-12715: IMC-Arches C6 at 8.33A - Refinement with C6 symmetry of the Inner... -

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Basic information

Entry
Database: EMDB / ID: EMD-12715
TitleIMC-Arches C6 at 8.33A - Refinement with C6 symmetry of the Inner Membrane Complex (IMC) with the Arches from the fully-assembled R388 type IV secretion system.
Map dataInner Membrane Complex (IMC) with the Arches, 6-fold symmetry and sharpened map
Sample
  • Complex: Type IV secretion system complexSecretion
    • Protein or peptide: TrwM protein
    • Protein or peptide: TrwK protein
    • Protein or peptide: TrwG protein
Function / homology
Function and homology information


protein secretion by the type IV secretion system / membrane => GO:0016020 / ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
Type IV secretion system, VirB3 / TrbD / AvhB / Type IV secretory pathway, VirB3-like protein / CagE, TrbE, VirB component of type IV transporter system, central domain / CagE, TrbE, VirB family, component of type IV transporter system / CagE, TrbE, VirB component of type IV transporter system / TraG, P-loop domain / TraG P-loop domain / Type IV secretion system protein VirB8/PtlE / Bacterial virulence protein VirB8 / VirB8 protein ...Type IV secretion system, VirB3 / TrbD / AvhB / Type IV secretory pathway, VirB3-like protein / CagE, TrbE, VirB component of type IV transporter system, central domain / CagE, TrbE, VirB family, component of type IV transporter system / CagE, TrbE, VirB component of type IV transporter system / TraG, P-loop domain / TraG P-loop domain / Type IV secretion system protein VirB8/PtlE / Bacterial virulence protein VirB8 / VirB8 protein / NTF2-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
TrwM protein / Type IV secretion system protein virB4 / TrwG protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.6 Å
AuthorsMace K / Vadakkepat AK / Lukoyanova N / Waksman G
Funding support United Kingdom, 4 items
OrganizationGrant numberCountry
Wellcome Trust098302 United Kingdom
Wellcome Trust217089 United Kingdom
Wellcome Trust202679/Z/16/Z United Kingdom
Wellcome Trust206166/Z/17/Z United Kingdom
CitationJournal: Nature / Year: 2022
Title: Cryo-EM structure of a type IV secretion system.
Authors: Kévin Macé / Abhinav K Vadakkepat / Adam Redzej / Natalya Lukoyanova / Clasien Oomen / Nathalie Braun / Marta Ukleja / Fang Lu / Tiago R D Costa / Elena V Orlova / David Baker / Qian Cong ...Authors: Kévin Macé / Abhinav K Vadakkepat / Adam Redzej / Natalya Lukoyanova / Clasien Oomen / Nathalie Braun / Marta Ukleja / Fang Lu / Tiago R D Costa / Elena V Orlova / David Baker / Qian Cong / Gabriel Waksman /
Abstract: Bacterial conjugation is the fundamental process of unidirectional transfer of DNAs, often plasmid DNAs, from a donor cell to a recipient cell. It is the primary means by which antibiotic resistance ...Bacterial conjugation is the fundamental process of unidirectional transfer of DNAs, often plasmid DNAs, from a donor cell to a recipient cell. It is the primary means by which antibiotic resistance genes spread among bacterial populations. In Gram-negative bacteria, conjugation is mediated by a large transport apparatus-the conjugative type IV secretion system (T4SS)-produced by the donor cell and embedded in both its outer and inner membranes. The T4SS also elaborates a long extracellular filament-the conjugative pilus-that is essential for DNA transfer. Here we present a high-resolution cryo-electron microscopy (cryo-EM) structure of a 2.8 megadalton T4SS complex composed of 92 polypeptides representing 8 of the 10 essential T4SS components involved in pilus biogenesis. We added the two remaining components to the structural model using co-evolution analysis of protein interfaces, to enable the reconstitution of the entire system including the pilus. This structure describes the exceptionally large protein-protein interaction network required to assemble the many components that constitute a T4SS and provides insights on the unique mechanism by which they elaborate pili.
History
DepositionApr 4, 2021-
Header (metadata) releaseJun 22, 2022-
Map releaseJun 22, 2022-
UpdateJul 20, 2022-
Current statusJul 20, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_12715.png

Downloads & links

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Map

FileDownload / File: emd_12715.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationInner Membrane Complex (IMC) with the Arches, 6-fold symmetry and sharpened map
Voxel sizeX=Y=Z: 2.134 Å
Density
Contour LevelBy AUTHOR: 1.2
Minimum - Maximum-1.654259 - 3.9017806
Average (Standard dev.)0.04615081 (±0.23072453)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 546.304 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_12715_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Inner Membrane Complex (IMC) with the Arches, 6-fold...

Fileemd_12715_additional_1.map
AnnotationInner Membrane Complex (IMC) with the Arches, 6-fold symmetry and unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Inner Membrane Complex (IMC) with the Arches, 6-fold...

Fileemd_12715_half_map_1.map
AnnotationInner Membrane Complex (IMC) with the Arches, 6-fold symmetry - Half_B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Inner Membrane Complex (IMC) with the Arches, 6-fold...

Fileemd_12715_half_map_2.map
AnnotationInner Membrane Complex (IMC) with the Arches, 6-fold symmetry - Half_A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Type IV secretion system complex

EntireName: Type IV secretion system complexSecretion
Components
  • Complex: Type IV secretion system complexSecretion
    • Protein or peptide: TrwM protein
    • Protein or peptide: TrwK protein
    • Protein or peptide: TrwG protein

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Supramolecule #1: Type IV secretion system complex

SupramoleculeName: Type IV secretion system complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli) / Strain: R388 plasmid
Recombinant expressionOrganism: Escherichia coli (E. coli)
Recombinant plasmid: pBADM11_trwN/virB1-trwE/virB10Strep_rbstrwD/virB11_rbsHistrwB /virD4
Molecular weightTheoretical: 2.808 MDa

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Macromolecule #1: TrwM protein

MacromoleculeName: TrwM protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 12.292585 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKPPQQQHEA FPLFKGATRL PTIWGVPMIP LMAMVMGVAV IALTVSIWWW ALVPPLWFIM AQITKNDDKA FRIWWLWIDT KFRNRNKGF WGASSYSPAN YRKRR

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Macromolecule #2: TrwK protein

MacromoleculeName: TrwK protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 93.76993 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGAIESRKLL ASETPVGQFI PYSHHVTDTI ISTKNAEYLS VWKIDGRSHQ SASEADVFQW IRELNNTLRG ISSANLSLWT HIVRRRVYE YPDAEFDNVF CRQLDEKYRE SFTGYNLMVN DLYLTVVYRP VSDKVLSFFA KRERETPDQK KHRQESCIKA L EDINRTLG ...String:
MGAIESRKLL ASETPVGQFI PYSHHVTDTI ISTKNAEYLS VWKIDGRSHQ SASEADVFQW IRELNNTLRG ISSANLSLWT HIVRRRVYE YPDAEFDNVF CRQLDEKYRE SFTGYNLMVN DLYLTVVYRP VSDKVLSFFA KRERETPDQK KHRQESCIKA L EDINRTLG QSFKRYGAEL LSVYEKGGHA FSAPLEFLAR LVNGEHIPMP ICRDRFSDYM AVNRPMFSKW GEVGELRSLT GL RRFGMLE IREYDDATEP GQLNVLLESD YEFVLTHSFS VLSRPAAKEY LQRHQKNLID ARDVATDQIE EIDEALNQLI SGH FVMGEH HCTLTVYGET VQQVRDNLAH ASAAMLDVAV LPKPVDLALE AGYWAQLPAN WQWRPRPAPI TSLNFLSFSP FHNF MSGKP TGNPWGPAVT ILKTVSGTPL YFNFHASKEE EDATDKRLLG NTMLIGQSSS GKTVLLGFLL AQAQKFKPTI VAFDK DRGM EISIRAMGGR YLPLKTGEPS GFNPFQLPPT HANLIFLKQF VKKLAAAGGE VTHRDEEEID QAITAMMSDS IDKSLR RLS LLLQFLPNPR SDDMDARPTV HARLVKWCEG GDYGWLFDNP TDALDLSTHQ IYGFDITEFL DNPEARTPVM MYLLYRT ES MIDGRRFMYV FDEFWKPLQD EYFEDLAKNK QKTIRKQNGI FVFATQEPSD ALESNIAKTL IQQCATYIFL ANPKADYE D YTQGFKLTDS EFELVRGLGE FSRRFLIKQG DQSALAEMNL GKFRTIVDGE TVERDFDDEL LVLSGTPDNA EIAESIIAE VGDDPAVWLP IFLDRVKAER SDV

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Macromolecule #3: TrwG protein

MacromoleculeName: TrwG protein / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 25.799994 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSKKQPKPVK AEQLKSYYEE SRGLERDLIG EFVKSRKTAW RVATASGLFG LLGMVCGIVG FSQPAPAPLV LRVDNATGAV DVVTTLREH ESSYGEVVDT YWLNQYVLNR EAYDYNTIQM NYDTTALLSA PAVQQDYYKL FDGSNARDRV LGNKARITVR V RSIQPNGR ...String:
MSKKQPKPVK AEQLKSYYEE SRGLERDLIG EFVKSRKTAW RVATASGLFG LLGMVCGIVG FSQPAPAPLV LRVDNATGAV DVVTTLREH ESSYGEVVDT YWLNQYVLNR EAYDYNTIQM NYDTTALLSA PAVQQDYYKL FDGSNARDRV LGNKARITVR V RSIQPNGR GQATVRFTTQ QHNSNGTVEA PQHQIATIGY TYIGAPMRSS DRLLNPLGFQ VTSYRADPEI LNN

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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: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 57.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: CryoSPARC ab-initio
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: OTHER / Details: Stochastic gradient descent (SGD)
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 7.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 126975

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