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- PDB-8rtd: Stalk-Arches-IMC structure from the fully-assembled R388 type IV ... -

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Basic information

Entry
Database: PDB / ID: 8rtd
TitleStalk-Arches-IMC structure from the fully-assembled R388 type IV secretion system determined by cryo-EM.
Components
  • TrwE protein
  • TrwG protein
  • TrwI protein
  • TrwJ protein
  • TrwM protein
  • Type IV secretion system protein virB4
KeywordsMEMBRANE PROTEIN / type IV secretion system type 4 secretion system T4SS Arches Stalk inner membrane complex IMC R388 plasmid conjugation bacterial secretion secretion secretion system protein complex VirB3 VirB4 VirB5 VirB6 VirB8 VirB10 TrwM TrwK TrwJ TrwI TrwG TrwE
Function / homology
Function and homology information


protein secretion by the type IV secretion system / ATP binding / membrane / plasma membrane
Similarity search - Function
Type IV secretion system, VirB5 / Type IV secretion system, VirB5-domain / Type IV secretion system proteins / Plasmid conjugal transfer TrbL/VirB6 / Type IV secretion system, VirB3 / TrbD / AvhB / TrbL/VirB6 plasmid conjugal transfer protein / 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 ...Type IV secretion system, VirB5 / Type IV secretion system, VirB5-domain / Type IV secretion system proteins / Plasmid conjugal transfer TrbL/VirB6 / Type IV secretion system, VirB3 / TrbD / AvhB / TrbL/VirB6 plasmid conjugal transfer protein / 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, VirB10/TrbI / Bacterial conjugation TrbI-like protein / Type IV secretion system, VirB10 / TraB / TrbI / NTF2-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
TrwM protein / Type IV secretion system protein virB4 / TrwJ protein / TrwI protein / TrwG protein / TrwE protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.33 Å
AuthorsMace, K. / Waksman, G.
Funding support United Kingdom, 4items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 1.2Aug 14, 2024Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TrwJ protein
D: TrwG protein
B: TrwJ protein
F: TrwG protein
C: TrwJ protein
G: TrwG protein
K: TrwJ protein
a: TrwE protein
E: TrwJ protein
L: TrwI protein
M: TrwI protein
j: TrwM protein
H: TrwI protein
O: Type IV secretion system protein virB4
I: TrwI protein
P: Type IV secretion system protein virB4
J: TrwI protein
Q: TrwG protein
R: TrwM protein
S: TrwG protein
T: Type IV secretion system protein virB4
U: TrwG protein
V: Type IV secretion system protein virB4
X: TrwG protein
Y: TrwG protein
Z: TrwE protein
b: TrwG protein
c: TrwG protein
d: TrwG protein
e: TrwE protein
f: TrwM protein
g: Type IV secretion system protein virB4
h: Type IV secretion system protein virB4
i: TrwG protein


Theoretical massNumber of molelcules
Total (without water)1,339,00234
Polymers1,339,00234
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 6 types, 34 molecules ABCKEDFGQSUXYbcdiaZeLMHIJjRfOP...

#1: Protein
TrwJ protein


Mass: 25190.461 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: Sequence from conjugative plasmid R388 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trwJ / Production host: Escherichia coli (E. coli) / References: UniProt: A8R752
#2: Protein
TrwG protein


Mass: 25799.994 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: Sequence from conjugative plasmid R388 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trwG / Production host: Escherichia coli (E. coli) / References: UniProt: A8R756
#3: Protein TrwE protein


Mass: 42443.785 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Sequence from conjugative plasmid R388 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trwE / Production host: Escherichia coli (E. coli) / References: UniProt: A8R758
#4: Protein
TrwI protein


Mass: 35324.172 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: Sequence from conjugative plasmid R388 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trwI / Production host: Escherichia coli (E. coli) / References: UniProt: A8R754
#5: Protein TrwM protein


Mass: 12292.585 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Sequence from conjugative plasmid R388 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trwM / Production host: Escherichia coli (E. coli) / References: UniProt: A8R750
#6: Protein
Type IV secretion system protein virB4


Mass: 93769.930 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Sequence from conjugative plasmid R388 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trwK / Production host: Escherichia coli (E. coli) / References: UniProt: A8R751

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Stalk-Arches-IMC complex from the fully-assembled R388 type IV secretion system
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 3300 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 57.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
2PHENIX1.18.2_3874:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 65173 / Symmetry type: POINT

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