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- EMDB-19481: Conformation-B of the full-length outer membrane core complex (Tr... -

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Basic information

Entry
Database: EMDB / ID: EMD-19481
TitleConformation-B of the full-length outer membrane core complex (TrwH/VirB7, TrwF/VirB9, TrwE/VirB10CTD) from the fully-assembled R388 type IV secretion system determined by cryo-EM.
Map dataOMCC_Conformation-B _ Unsharpened
Sample
  • Complex: Conformation-B of the outer membrane core complex from the fully-assembled R388 type IV secretion system
    • Protein or peptide: TrwE protein
    • Protein or peptide: TrwF protein
    • Protein or peptide: TrwH
Keywordstype IV secretion system type 4 secretion system T4SS OMCC Conformation-B core complex outer membrane complex R388 plasmid conjugation bacterial secretion secretion secretion system protein complex VirB10 VirB9 VirB7 TrwE TrwF TrwH / MEMBRANE PROTEIN
Function / homology
Function and homology information


P-type conjugative transfer protein VirB9 / : / Conjugal transfer, TrbG/VirB9/CagX / VirB9/CagX/TrbG, C-terminal / VirB9/CagX/TrbG, C-terminal domain superfamily / Conjugal transfer protein / Type IV secretion system, VirB10/TrbI / Bacterial conjugation TrbI-like protein / Type IV secretion system, VirB10 / TraB / TrbI / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
TrwH / TrwF protein / TrwE protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsMace K / 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: EMBO J / Year: 2024
Title: Cryo-EM structure of a conjugative type IV secretion system suggests a molecular switch regulating pilus biogenesis.
Authors: Kévin Macé / Gabriel Waksman /
Abstract: Conjugative type IV secretion systems (T4SS) mediate bacterial conjugation, a process that enables the unidirectional exchange of genetic materials between a donor and a recipient bacterial cell. ...Conjugative type IV secretion systems (T4SS) mediate bacterial conjugation, a process that enables the unidirectional exchange of genetic materials between a donor and a recipient bacterial cell. Bacterial conjugation is the primary means by which antibiotic resistance genes spread among bacterial populations (Barlow 2009; Virolle et al, 2020). Conjugative T4SSs form pili: long extracellular filaments that connect with recipient cells. Previously, we solved the cryo-electron microscopy (cryo-EM) structure of a conjugative T4SS. In this article, based on additional data, we present a more complete T4SS cryo-EM structure than that published earlier. Novel structural features include details of the mismatch symmetry within the OMCC, the presence of a fourth VirB8 subunit in the asymmetric unit of both the arches and the inner membrane complex (IMC), and a hydrophobic VirB5 tip in the distal end of the stalk. Additionally, we provide previously undescribed structural insights into the protein VirB10 and identify a novel regulation mechanism of T4SS-mediated pilus biogenesis by this protein, that we believe is a key checkpoint for this process.
History
DepositionJan 25, 2024-
Header (metadata) releaseJun 19, 2024-
Map releaseJun 19, 2024-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19481.png

Downloads & links

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Map

FileDownload / File: emd_19481.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOMCC_Conformation-B _ Unsharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 300 pix.
= 320.1 Å		1.07 Å/pix.
x 300 pix.
= 320.1 Å		1.07 Å/pix.
x 300 pix.
= 320.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.067 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.26813614 - 1.0659198
Average (Standard dev.)0.022237409 (±0.06991796)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 320.1 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19481_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: OMCC Conformation-B Sharpened

Fileemd_19481_additional_1.map
AnnotationOMCC_Conformation-B _ Sharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-A

Fileemd_19481_half_map_1.map
AnnotationHalf-A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-B

Fileemd_19481_half_map_2.map
AnnotationHalf-B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Conformation-B of the outer membrane core complex from the fully-...

EntireName: Conformation-B of the outer membrane core complex from the fully-assembled R388 type IV secretion system
Components
  • Complex: Conformation-B of the outer membrane core complex from the fully-assembled R388 type IV secretion system
    • Protein or peptide: TrwE protein
    • Protein or peptide: TrwF protein
    • Protein or peptide: TrwH

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Supramolecule #1: Conformation-B of the outer membrane core complex from the fully-...

SupramoleculeName: Conformation-B of the outer membrane core complex from the fully-assembled R388 type IV secretion system
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: TrwE protein

MacromoleculeName: TrwE protein / type: protein_or_peptide / ID: 1 / Details: Sequence from conjugative plasmid R388 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 42.443785 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MFGRKKGDVI DAGAELERAE QERIEGEYGA SELASERRPH TPGARTLLMV LLCVIAVVLV TLSYKAYKVR GVVEDDDAQP QQVVRQVIP GYTPRPIRPE PENVPEPPQP TTSVPAIQPA PVTQPVRPQP TGPREKTPYE LARERMLRSG LTAGSGGGED L PRPQGGDV ...String:
MFGRKKGDVI DAGAELERAE QERIEGEYGA SELASERRPH TPGARTLLMV LLCVIAVVLV TLSYKAYKVR GVVEDDDAQP QQVVRQVIP GYTPRPIRPE PENVPEPPQP TTSVPAIQPA PVTQPVRPQP TGPREKTPYE LARERMLRSG LTAGSGGGED L PRPQGGDV PAGGLMGGGG GGGELAEKLQ PMRLSGSSAG RLGNRDMLIT QGTQLDCVLE TRLVTTQPGM TTCHLTRDVY ST SGRVVLL DRGSKVVGFY QGGLRQGQAR IFVQWSRIET PSGVVINLDS PGTGPLGEAG LGGWIDRHFW ERFGGAIMIS LIG DLGDWA SRQGSRQGDN SIQFSNTANG VESAAAEALR NSINIPPTLY KNQGERVNIL VARDLDFSDV YSLESIPTK

UniProtKB: TrwE protein

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Macromolecule #2: TrwF protein

MacromoleculeName: TrwF protein / type: protein_or_peptide / ID: 2 / Details: Sequence from conjugative plasmid R388 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 29.749586 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKLAIVALL ASLHAVPALA LDVPSSSRYD HRIRYVTYNP ADVVQVDTVL GVATHIMLEE GEQYLTHAFG DSEAYAFARK GRHIFIKPQ AELANTNLIV VTDRRSYKFR LQMRNDRNGA MYELAFRYPD TQARQTREAN ARAAVEAAFE QRVGAYYNLK Y MMSGDKDI ...String:
MKKLAIVALL ASLHAVPALA LDVPSSSRYD HRIRYVTYNP ADVVQVDTVL GVATHIMLEE GEQYLTHAFG DSEAYAFARK GRHIFIKPQ AELANTNLIV VTDRRSYKFR LQMRNDRNGA MYELAFRYPD TQARQTREAN ARAAVEAAFE QRVGAYYNLK Y MMSGDKDI APVNAWDDGR FTYFKFSANA DLPSIYFVDA EGNESLVPRT TVGSSNNIIA VHKVNPKWMI RLGNRALAIF NE AYDPNGV PNDTGTASPA VRRVNKGGN

UniProtKB: TrwF protein

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Macromolecule #3: TrwH

MacromoleculeName: TrwH / type: protein_or_peptide / ID: 3 / Details: Sequence from conjugative plasmid R388 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 5.089048 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKTIIFAILM TGLLSACASA PKPKQPSDFN REPVNKTVPV EIQRGAL

UniProtKB: TrwH

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 57.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 3.3000000000000003 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 533530
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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