[English] 日本語
Yorodumi
- PDB-7oko: Structure of the outer-membrane core complex (outer ring) from a ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7oko
TitleStructure of the outer-membrane core complex (outer ring) from a conjugative type IV secretion system
Components
  • TraB
  • Type IV conjugative transfer system lipoprotein TraV
  • Type-F conjugative transfer system secretin TraK
KeywordsMEMBRANE PROTEIN / Type IV secretion system / F plasmid / outer-membrane core complex / conjugation
Function / homologyPilus 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) / Type-F conjugative transfer system secretin TraK / Type IV conjugative transfer system lipoprotein TraV
Function and homology information
Biological speciesSalmonella enterica (bacteria)
Salmonella enterica subsp. salamae serovar 58:l
z13
z28:z6
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsAmin, H. / Ilangovan, A. / Costa, T.R.D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust215164/Z/18/Z United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: Architecture of the outer-membrane core complex from a conjugative type IV secretion system.
Authors: Himani Amin / Aravindan Ilangovan / Tiago R D Costa /
Abstract: Conjugation is one of the most important processes that bacteria utilize to spread antibiotic resistance genes among bacterial populations. Interbacterial DNA transfer requires a large double ...Conjugation is one of the most important processes that bacteria utilize to spread antibiotic resistance genes among bacterial populations. Interbacterial DNA transfer requires a large double membrane-spanning nanomachine called the type 4 secretion system (T4SS) made up of the inner-membrane complex (IMC), the outer-membrane core complex (OMCC) and the conjugative pilus. The iconic F plasmid-encoded T4SS has been central in understanding conjugation for several decades, however atomic details of its structure are not known. Here, we report the structure of a complete conjugative OMCC encoded by the pED208 plasmid from E. coli, solved by cryo-electron microscopy at 3.3 Å resolution. This 2.1 MDa complex has a unique arrangement with two radial concentric rings, each having a different symmetry eventually contributing to remarkable differences in protein stoichiometry and flexibility in comparison to other OMCCs. Our structure suggests that F-OMCC is a highly dynamic complex, with implications for pilus extension and retraction during conjugation.
History
DepositionMay 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-12963
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-12963
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AA: Type IV conjugative transfer system lipoprotein TraV
AB: Type IV conjugative transfer system lipoprotein TraV
AC: TraB
0: Type IV conjugative transfer system lipoprotein TraV
1: Type IV conjugative transfer system lipoprotein TraV
2: TraB
3: Type-F conjugative transfer system secretin TraK
4: Type-F conjugative transfer system secretin TraK
5: Type IV conjugative transfer system lipoprotein TraV
6: Type IV conjugative transfer system lipoprotein TraV
7: TraB
8: Type-F conjugative transfer system secretin TraK
9: Type-F conjugative transfer system secretin TraK
A: Type-F conjugative transfer system secretin TraK
B: Type-F conjugative transfer system secretin TraK
C: Type IV conjugative transfer system lipoprotein TraV
D: Type IV conjugative transfer system lipoprotein TraV
E: TraB
F: Type-F conjugative transfer system secretin TraK
G: Type-F conjugative transfer system secretin TraK
H: Type IV conjugative transfer system lipoprotein TraV
I: Type IV conjugative transfer system lipoprotein TraV
J: TraB
K: Type-F conjugative transfer system secretin TraK
L: Type-F conjugative transfer system secretin TraK
M: Type IV conjugative transfer system lipoprotein TraV
N: Type IV conjugative transfer system lipoprotein TraV
O: TraB
P: Type-F conjugative transfer system secretin TraK
Q: Type-F conjugative transfer system secretin TraK
R: Type IV conjugative transfer system lipoprotein TraV
S: Type IV conjugative transfer system lipoprotein TraV
T: TraB
U: Type-F conjugative transfer system secretin TraK
V: Type-F conjugative transfer system secretin TraK
W: Type IV conjugative transfer system lipoprotein TraV
X: Type IV conjugative transfer system lipoprotein TraV
Y: TraB
Z: Type-F conjugative transfer system secretin TraK
a: Type-F conjugative transfer system secretin TraK
b: Type IV conjugative transfer system lipoprotein TraV
c: Type IV conjugative transfer system lipoprotein TraV
d: TraB
e: Type-F conjugative transfer system secretin TraK
f: Type-F conjugative transfer system secretin TraK
g: Type IV conjugative transfer system lipoprotein TraV
h: Type IV conjugative transfer system lipoprotein TraV
i: TraB
j: Type-F conjugative transfer system secretin TraK
k: Type-F conjugative transfer system secretin TraK
l: Type IV conjugative transfer system lipoprotein TraV
m: Type IV conjugative transfer system lipoprotein TraV
n: TraB
o: Type-F conjugative transfer system secretin TraK
p: Type-F conjugative transfer system secretin TraK
q: Type IV conjugative transfer system lipoprotein TraV
r: Type IV conjugative transfer system lipoprotein TraV
s: TraB
t: Type-F conjugative transfer system secretin TraK
u: Type-F conjugative transfer system secretin TraK
v: Type IV conjugative transfer system lipoprotein TraV
w: Type IV conjugative transfer system lipoprotein TraV
x: TraB
y: Type-F conjugative transfer system secretin TraK
z: Type-F conjugative transfer system secretin TraK


Theoretical massNumber of molelcules
Total (without water)1,164,93865
Polymers1,164,93865
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area165080 Å2
ΔGint-904 kcal/mol
Surface area317380 Å2
MethodPISA

-
Components

#1: Protein ...
Type IV conjugative transfer system lipoprotein TraV / TraV


Mass: 20928.650 Da / Num. of mol.: 26
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria) / Gene: traV, GND40_003952 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A753A8N9
#2: Protein/peptide
TraB /


Mass: 1128.233 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria) / Production host: Escherichia coli (E. coli)
#3: Protein ...
Type-F conjugative transfer system secretin TraK


Mass: 23312.551 Da / Num. of mol.: 26
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. salamae serovar 58:l,z13,z28:z6 (bacteria)
Gene: traK, G4J24_003123 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A734HNY4

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Outer-membrane core complex (outer ring) / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Salmonella enterica (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
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: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1.3 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 298235 / 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