[English] 日本語
Yorodumi
- PDB-7spb: Models for C13 reconstruction of Outer Membrane Core Complex (OMC... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7spb
TitleModels for C13 reconstruction of Outer Membrane Core Complex (OMCC) of Type IV Secretion System (T4SS) encoded by F-plasmid (pED208).
Components
  • TraB
  • TraK
  • TraV
KeywordsSTRUCTURAL PROTEIN / Symmetry alteration / Symmetry mismatch / Drug resistance / Type IV secretion system (T4SS)
Function / homology
Function and homology information


Pilus assembly TraK / Type-F conjugative transfer system secretin TraK / TraK protein / Type IV conjugative transfer system protein TraV / Type IV conjugative transfer system lipoprotein (TraV) / Bacterial conjugation TrbI-like protein / Type IV secretion system, VirB10 / TraB / TrbI / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Biological speciesSalmonella typhi (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.31 Å
AuthorsLiu, X. / Khara, P. / Baker, M.L. / Christie, P.J. / Hu, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2022
Title: Structure of a type IV secretion system core complex encoded by multi-drug resistance F plasmids.
Authors: Xiangan Liu / Pratick Khara / Matthew L Baker / Peter J Christie / Bo Hu /
Abstract: Bacterial type IV secretion systems (T4SSs) are largely responsible for the proliferation of multi-drug resistance. We solved the structure of the outer-membrane core complex (OMCC) of a T4SS encoded ...Bacterial type IV secretion systems (T4SSs) are largely responsible for the proliferation of multi-drug resistance. We solved the structure of the outer-membrane core complex (OMCC) of a T4SS encoded by a conjugative F plasmid at <3.0 Å resolution by cryoelectron microscopy. The OMCC consists of a 13-fold symmetrical outer ring complex (ORC) built from 26 copies of TraK and TraV C-terminal domains, and a 17-fold symmetrical central cone (CC) composed of 17 copies of TraB β-barrels. Domains of TraV and TraB also bind the CC and ORC substructures, establishing that these proteins undergo an intraprotein symmetry alteration to accommodate the C13:C17 symmetry mismatch. We present evidence that other pED208-encoded factors stabilize the C13:C17 architecture and define the importance of TraK, TraV and TraB domains to T4SS function. This work identifies OMCC structural motifs of proposed importance for structural transitions associated with F plasmid dissemination and F pilus biogenesis.
History
DepositionNov 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-24769
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-24769
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A1: TraV
A2: TraV
A3: TraV
A4: TraV
A5: TraV
A6: TraV
A7: TraV
A8: TraV
A9: TraV
A10: TraV
A11: TraV
A12: TraV
A13: TraV
B1: TraV
B2: TraV
B3: TraV
B4: TraV
B5: TraV
B6: TraV
B7: TraV
B8: TraV
B9: TraV
B10: TraV
B11: TraV
B12: TraV
B13: TraV
C1: TraK
C2: TraK
C3: TraK
C4: TraK
C5: TraK
C6: TraK
C7: TraK
C8: TraK
C9: TraK
C10: TraK
C11: TraK
C12: TraK
C13: TraK
D1: TraK
D2: TraK
D3: TraK
D4: TraK
D5: TraK
D6: TraK
D7: TraK
D8: TraK
D9: TraK
D10: TraK
D11: TraK
D12: TraK
D13: TraK
E1: TraB
E2: TraB
E3: TraB
E4: TraB
E5: TraB
E6: TraB
E7: TraB
E8: TraB
E9: TraB
E10: TraB
E11: TraB
E12: TraB
E13: TraB
F1: TraB
F2: TraB
F3: TraB
F4: TraB
F5: TraB
F6: TraB
F7: TraB
F8: TraB
F9: TraB
F10: TraB
F11: TraB
F12: TraB
F13: TraB


Theoretical massNumber of molelcules
Total (without water)2,478,76478
Polymers2,478,76478
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein ...
TraV


Mass: 20928.650 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Source: (natural) Salmonella typhi (bacteria) / Plasmid details: pED208 / References: UniProt: Q8KNL2
#2: Protein ...
TraK


Mass: 26648.465 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Source: (natural) Salmonella typhi (bacteria) / Plasmid details: pED208 / References: UniProt: Q8KNL8
#3: Protein ...
TraB


Mass: 47759.957 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Source: (natural) Salmonella typhi (bacteria) / Plasmid details: pED208 / References: UniProt: Q8KNL7

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Outer membrane core complex of T4SS encoded by F plasmid (pED208)
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

EM software
IDNameCategory
4cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C13 (13 fold cyclic)
3D reconstructionResolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 70700 / Symmetry type: POINT

+
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