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- EMDB-12717: Dimer TrwK/VirB4unbound C1 at 3.49A - Local refinement without sy... -

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Basic information

Entry
Database: EMDB / ID: EMD-12717
TitleDimer TrwK/VirB4unbound C1 at 3.49A - Local refinement without symmetry of the TrwK/VirB4unbound dimer complex from the R388 type IV secretion system.
Map dataLocal refinement TrwK/VirB4unbound dimer complex without symmetry sharpened map
Sample
  • Complex: Hexamer complex of Apo-TrwK/VirB4 with Hcp1
    • Protein or peptide: TrwK protein
Keywordstype IV secretion system / type 4 secretion system / T4SS / inner membrane complex / inner membrane / R388 plasmid / conjugation / ATPase / bacterial secretion / secretion / secretion system / protein complex / VirB4 / TrwK / dimer / Hcp / MEMBRANE PROTEIN
Function / homology
Function and homology information


ATP hydrolysis activity / ATP binding
Similarity search - Function
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 / : / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Type IV secretion system protein virB4
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsVadakkepat AK / Mace K
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 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_12717.png

Downloads & links

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Map

FileDownload / File: emd_12717.map.gz / Format: CCP4 / Size: 7.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal refinement TrwK/VirB4unbound dimer complex without symmetry sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.05 Å/pix.
x 134 pix.
= 140.432 Å		1.05 Å/pix.
x 90 pix.
= 94.32 Å		1.05 Å/pix.
x 163 pix.
= 170.824 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.048 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 8.0
Minimum - Maximum-26.988347999999998 - 81.720370000000003
Average (Standard dev.)0.47296843 (±2.800809)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin635283
Dimensions90163134
Spacing13490163
CellA: 140.43199 Å / B: 94.32 Å / C: 170.82399 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Local refinement TrwK/VirB4unbound dimer complex without symmetry unsharpened...

Fileemd_12717_additional_1.map
AnnotationLocal refinement TrwK/VirB4unbound dimer complex without symmetry unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Local refinement TrwK/VirB4unbound dimer complex - Half-A

Fileemd_12717_half_map_1.map
AnnotationLocal refinement TrwK/VirB4unbound dimer complex - Half-A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Local refinement TrwK/VirB4unbound dimer complex - Half-B

Fileemd_12717_half_map_2.map
AnnotationLocal refinement TrwK/VirB4unbound dimer complex - Half-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 : Hexamer complex of Apo-TrwK/VirB4 with Hcp1

EntireName: Hexamer complex of Apo-TrwK/VirB4 with Hcp1
Components
  • Complex: Hexamer complex of Apo-TrwK/VirB4 with Hcp1
    • Protein or peptide: TrwK protein

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Supramolecule #1: Hexamer complex of Apo-TrwK/VirB4 with Hcp1

SupramoleculeName: Hexamer complex of Apo-TrwK/VirB4 with Hcp1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: TrwK protein

MacromoleculeName: TrwK protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 94.202328 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 SDVGSGSGS

UniProtKB: Type IV secretion system protein virB4

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: CryoSPARC ab-initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 214048
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: OTHER / Details: Stochastic gradient descent (SGD)

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