[English] 日本語
Yorodumi
- PDB-7o3j: O-layer structure (TrwH/VirB7, TrwF/VirB9CTD, TrwE/VirB10CTD) of ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7o3j
TitleO-layer structure (TrwH/VirB7, TrwF/VirB9CTD, TrwE/VirB10CTD) of the outer membrane core complex 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 / O-layer / core complex / outer membrane complex / inner membrane / 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: 2.6 Å
AuthorsMace, K. / Vadakkepat, A.K. / Lukoyanova, N. / 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: 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 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 23, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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


Theoretical massNumber of molelcules
Total (without water)1,081,95442
Polymers1,081,95442
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area185700 Å2
ΔGint-603 kcal/mol
Surface area178880 Å2

-
Components

#1: Protein
TrwE protein


Mass: 42443.785 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Details: R388 plasmid / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trwE
Plasmid: pBADM11_trwN/virB1-trwE/virB10Strep_rbstrwD/virB11_rbsHistrwB /virD4
Production host: Escherichia coli (E. coli) / References: UniProt: O50337
#2: Protein
TrwF protein


Mass: 29749.586 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Details: R388 plasmid / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trwF
Plasmid: pBADM11_trwN/virB1-trwE/virB10Strep_rbstrwD/virB11_rbsHistrwB /virD4
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: R388 plasmid / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trwH
Plasmid: pBADM11_trwN/virB1-trwE/virB10Strep_rbstrwD/virB11_rbsHistrwB /virD4
Production host: Escherichia coli (E. coli) / References: UniProt: O50334
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Type IV secretion system complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 2.808 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: R388 plasmid
Source (recombinant)Organism: Escherichia coli (E. coli)
Plasmid: pBADM11_trwN/virB1-trwE/virB10Strep_rbstrwD/virB11_rbsHistrwB /virD4
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

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

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C14 (14 fold cyclic)
3D reconstructionResolution: 2.6 Å / Num. of particles: 709769 / Symmetry type: POINT
Atomic model buildingPDB-ID: 3JQO

3jqo


Accession code: 3JQO / Source name: PDB / Type: experimental model

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more