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- EMDB-19483: Stalk C5 at 2.97A - Local refinement with C5 symmetry of the Stal... -

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Basic information

Entry
Database: EMDB / ID: EMD-19483
TitleStalk C5 at 2.97A - Local refinement with C5 symmetry of the Stalk complex from the fully-assembled R388 type IV secretion system.
Map dataStalk-C5 _ Unsharpened
Sample
  • Complex: Stalk complex from the fully-assembled R388 type IV secretion system
    • Protein or peptide: TrwJ protein
    • Protein or peptide: TrwI protein
Keywordstype IV secretion system type 4 secretion system T4SS Stalk R388 plasmid conjugation bacterial secretion secretion secretion system protein complex VirB5 VirB6 TrwI TrwJ / MEMBRANE PROTEIN
Function / homologyType IV secretion system, VirB5 / Type IV secretion system, VirB5-domain / Type IV secretion system proteins / Plasmid conjugal transfer TrbL/VirB6 / TrbL/VirB6 plasmid conjugal transfer protein / protein secretion by the type IV secretion system / membrane / TrwJ protein / TrwI protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 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-
UpdateAug 14, 2024-
Current statusAug 14, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19483.png

Downloads & links

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Map

FileDownload / File: emd_19483.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStalk-C5 _ Unsharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 512 pix.
= 546.304 Å		1.07 Å/pix.
x 512 pix.
= 546.304 Å		1.07 Å/pix.
x 512 pix.
= 546.304 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-0.6098682 - 1.510094
Average (Standard dev.)0.006588111 (±0.032924816)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 546.304 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19483_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Stalk-C5 Sharpened-deepEMhancer

Fileemd_19483_additional_1.map
AnnotationStalk-C5 _ Sharpened-deepEMhancer
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half-A

Fileemd_19483_half_map_1.map
AnnotationHalf-A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Half-B

Fileemd_19483_half_map_2.map
AnnotationHalf-B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Stalk complex from the fully-assembled R388 type IV secretion system

EntireName: Stalk complex from the fully-assembled R388 type IV secretion system
Components
  • Complex: Stalk complex from the fully-assembled R388 type IV secretion system
    • Protein or peptide: TrwJ protein
    • Protein or peptide: TrwI protein

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Supramolecule #1: Stalk complex from the fully-assembled R388 type IV secretion system

SupramoleculeName: Stalk 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: TrwJ protein

MacromoleculeName: TrwJ protein / type: protein_or_peptide / ID: 1 / Details: Sequence from conjugative plasmid R388 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 25.190461 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKLVMTAAV AAILGAASPV MAQGIPVFDG TRALDFVQQF ARMKEQLDTA KDQLAEAQRM YEAVTGGRGL GDLMRNAQLR EYLPDDLRT VYDSANGGGY SGISGSINDI LRDERLNGSV ADMRRSIEER SRTAAATDKA VGLRAYEGAQ QRLAQIEGLM D EISRTQDQ ...String:
MKKLVMTAAV AAILGAASPV MAQGIPVFDG TRALDFVQQF ARMKEQLDTA KDQLAEAQRM YEAVTGGRGL GDLMRNAQLR EYLPDDLRT VYDSANGGGY SGISGSINDI LRDERLNGSV ADMRRSIEER SRTAAATDKA VGLRAYEGAQ QRLAQIEGLM D EISRTQDQ KAIEELQARI AGEQAAIQNE TTKLQMIAQL RQAEQALISE QRRERNMRIL SSGNQGMPTI Q

UniProtKB: TrwJ protein

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Macromolecule #2: TrwI protein

MacromoleculeName: TrwI protein / type: protein_or_peptide / ID: 2 / Details: Sequence from conjugative plasmid R388 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 35.324172 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAFELFTPLF NKIDQTTATY VTDISSRAIA AITPVVSVGL TLGFITYGWL IIRGAVEMPV AEFLNRCLRI GIIVSIALAG GLYQGEIAN AITTVPDELA SALLGNPTQG ASAAALVDQS AQQGFDRASE AFEEAGFFSS DGLLYGLFGI IILLATGLLA A IGGAFLLL ...String:
MAFELFTPLF NKIDQTTATY VTDISSRAIA AITPVVSVGL TLGFITYGWL IIRGAVEMPV AEFLNRCLRI GIIVSIALAG GLYQGEIAN AITTVPDELA SALLGNPTQG ASAAALVDQS AQQGFDRASE AFEEAGFFSS DGLLYGLFGI IILLATGLLA A IGGAFLLL AKIALALLAG LGPLFILALI WQPTHRFFDQ WAQQVLNYGL LIVLFAAVFG LLMQIFGSYM ADLRFDGAQN VA YAIGGSV ILSIVSIVLL MQLPSIASGL AGGIGLGYMW ELRSMRSGAG AAMRGGRAMA RGARAAPGAA RGAAVGAANM AKT VATGGA GVARAAAGYF RGRKAG

UniProtKB: TrwI protein

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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: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 104720
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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