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- PDB-8rt8: Conformation-C of the full-length outer membrane core complex (Tr... -

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Basic information

Entry
Database: PDB / ID: 8rt8
TitleConformation-C 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.
Components
  • TrwE protein
  • TrwF protein
  • TrwH protein
KeywordsMEMBRANE PROTEIN / type IV secretion system type 4 secretion system T4SS OMCC Conformation-C core complex outer membrane complex R388 plasmid conjugation bacterial secretion secretion secretion system protein complex VirB10 VirB9 VirB7 TrwE TrwF TrwH
Function / homology
Function and homology information


: / 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 protein / TrwF protein / TrwE protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.05 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
Revision 1.3Oct 23, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TrwE protein
B: TrwF protein
C: TrwH protein
D: TrwE protein
E: TrwF protein
F: TrwH protein
G: TrwE protein
H: TrwF protein
I: TrwH protein
J: TrwE protein
K: TrwF protein
L: TrwH protein
M: TrwE protein
N: TrwF protein
O: TrwH protein
P: TrwE protein
Q: TrwF protein
R: TrwH protein
S: TrwE protein
T: TrwF protein
U: TrwH protein
V: TrwE protein
W: TrwF protein
X: TrwH protein
Y: TrwE protein
Z: TrwF protein
a: TrwH protein
b: TrwE protein
c: TrwF protein
d: TrwH protein
e: TrwE protein
f: TrwF protein
g: TrwH protein
h: TrwE protein
i: TrwF protein
j: TrwH protein
k: TrwE protein
l: TrwF protein
m: TrwH protein
n: TrwE protein
o: TrwF protein
p: TrwH protein
u: TrwE protein
v: TrwF protein
y: TrwE protein
z: TrwF protein


Theoretical massNumber of molelcules
Total (without water)1,226,34146
Polymers1,226,34146
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
TrwE protein


Mass: 42443.785 Da / Num. of mol.: 16
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: O50337
#2: Protein
TrwF protein


Mass: 29749.586 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Details: Sequence from conjugative plasmid R388 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trwF / Production host: Escherichia coli (E. coli) / References: UniProt: O50336
#3: Protein/peptide
TrwH protein


Mass: 5089.048 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Details: Sequence from conjugative plasmid R388 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trwH / Production host: Escherichia coli (E. coli) / References: UniProt: O50334
Has protein modificationY

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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: Conformation-C of the outer membrane core 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: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 530296 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00656894
ELECTRON MICROSCOPYf_angle_d0.68877022
ELECTRON MICROSCOPYf_dihedral_angle_d28.6358010
ELECTRON MICROSCOPYf_chiral_restr0.0468370
ELECTRON MICROSCOPYf_plane_restr0.00410214

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