[English] 日本語
Yorodumi
- PDB-8rtb: Extended inner membrane complex (IMC) protomer structure (TrwM/Vi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8rtb
TitleExtended inner membrane complex (IMC) protomer structure (TrwM/VirB3-TrwK/VirB4-TrwI/VirB6-TrwG/VirB8-TrwE/VirB10) from the fully-assembled R388 type IV secretion system determined by cryo-EM.
Components
  • TrwE protein
  • TrwG protein
  • TrwI protein
  • TrwK protein
  • TrwM protein
KeywordsMEMBRANE PROTEIN / type IV secretion system type 4 secretion system T4SS inner membrane complex IMC IMC-protomer Extended IMC R388 plasmid conjugation bacterial secretion secretion secretion system protein complex VirB3 VirB4 VirB6 VirB8 VirB10 TrwM TrwK TrwI TrwG TrwE
Function / homology
Function and homology information


protein secretion by the type IV secretion system / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
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 / : ...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 / TrwI protein / TrwG protein / TrwE protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.83 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: TrwM protein
A: TrwK protein
B: TrwK protein
E: TrwG protein
D: TrwG protein
F: TrwG protein
G: TrwG protein
H: TrwE protein
J: TrwI protein


Theoretical massNumber of molelcules
Total (without water)380,8009
Polymers380,8009
Non-polymers00
Water00
1


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

-
Components

#1: Protein TrwM protein


Mass: 12292.585 Da / Num. of mol.: 1
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: O50329
#2: Protein TrwK protein


Mass: 93769.930 Da / Num. of mol.: 2
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: O50330
#3: Protein
TrwG protein


Mass: 25799.994 Da / Num. of mol.: 4
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: O50335
#4: Protein TrwE protein


Mass: 42443.785 Da / Num. of mol.: 1
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
#5: Protein TrwI protein


Mass: 35324.172 Da / Num. of mol.: 1
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: O50333

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Extended IMC-protomer 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

-
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)

-
Processing

EM software
IDNameVersionCategory
2PHENIX1.18.2_3874:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 234578 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00514710
ELECTRON MICROSCOPYf_angle_d0.72519942
ELECTRON MICROSCOPYf_dihedral_angle_d26.0931990
ELECTRON MICROSCOPYf_chiral_restr0.0462185
ELECTRON MICROSCOPYf_plane_restr0.0062574

+
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