[English] 日本語
Yorodumi
- PDB-6ogd: Cryo-EM structure of YenTcA in its prepore state -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6ogd
TitleCryo-EM structure of YenTcA in its prepore state
Components
  • Chitinase 2
  • Toxin subunit YenA1
  • Toxin subunit YenA2
KeywordsTOXIN / Membrane protein Pore-forming toxin Complex
Function / homology
Function and homology information


chitinase / chitin catabolic process / chitinase activity / chitin binding / polysaccharide catabolic process / pathogenesis / extracellular region
Neuraminidase-like domain / Chitinase II / Tc toxin complex TcA C-terminal TcB-binding domain / Salmonella virulence plasmid 28.1kDa A protein / Glycosyl hydrolases family 18 / Chitinase insertion domain superfamily / Insecticidal toxin complex/plasmid virulence protein / Glycoside hydrolase superfamily / Glycoside hydrolase family 18, catalytic domain
Toxin subunit YenA1 / Toxin subunit YenA2 / Chitinase 2
Specimen sourceYersinia entomophaga (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsPiper, S.J. / Brillault, L. / Box, J.K. / Landsberg, M.J.
Funding supportAustralia , New Zealand , 4件
OrganizationGrant numberCountry
Australian Research CouncilDP170104484Australia
Australian Research CouncilDP160101018Australia
Royal Society of New Zealand14-UOA-146New Zealand
Foundation for Science and TechnologyC10X0804New Zealand
CitationJournal: Nat Commun / Year: 2019
Title: Cryo-EM structures of the pore-forming A subunit from the Yersinia entomophaga ABC toxin.
Authors: Sarah J Piper / Lou Brillault / Rosalba Rothnagel / Tristan I Croll / Joseph K Box / Irene Chassagnon / Sebastian Scherer / Kenneth N Goldie / Sandra A Jones / Femke Schepers / Lauren Hartley-Tassell / Thomas Ve / Jason N Busby / Julie E Dalziel / J Shaun Lott / Ben Hankamer / Henning Stahlberg / Mark R H Hurst / Michael J Landsberg /
Abstract: ABC toxins are pore-forming virulence factors produced by pathogenic bacteria. YenTcA is the pore-forming and membrane binding A subunit of the ABC toxin YenTc, produced by the insect pathogen ...ABC toxins are pore-forming virulence factors produced by pathogenic bacteria. YenTcA is the pore-forming and membrane binding A subunit of the ABC toxin YenTc, produced by the insect pathogen Yersinia entomophaga. Here we present cryo-EM structures of YenTcA, purified from the native source. The soluble pre-pore structure, determined at an average resolution of 4.4 Å, reveals a pentameric assembly that in contrast to other characterised ABC toxins is formed by two TcA-like proteins (YenA1 and YenA2) and decorated by two endochitinases (Chi1 and Chi2). We also identify conformational changes that accompany membrane pore formation by visualising YenTcA inserted into liposomes. A clear outward rotation of the Chi1 subunits allows for access of the protruding translocation pore to the membrane. Our results highlight structural and functional diversity within the ABC toxin subfamily, explaining how different ABC toxins are capable of recognising diverse hosts.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 2, 2019 / Release: May 8, 2019Array

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-20053
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Toxin subunit YenA1
B: Toxin subunit YenA2
C: Chitinase 2
D: Toxin subunit YenA1
E: Toxin subunit YenA2
F: Chitinase 2
G: Toxin subunit YenA1
H: Toxin subunit YenA2
I: Chitinase 2
J: Toxin subunit YenA1
K: Toxin subunit YenA2
L: Chitinase 2
M: Toxin subunit YenA1
N: Toxin subunit YenA2
O: Chitinase 2


Theoretical massNumber of molelcules
Total (without water)1,779,88915
Polymers1,779,88915
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein/peptide
Toxin subunit YenA1 /


Mass: 129912.320 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Yersinia entomophaga (bacteria) / References: UniProt: B6A877
#2: Protein/peptide
Toxin subunit YenA2 /


Mass: 156324.938 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Yersinia entomophaga (bacteria) / References: UniProt: B6A878
#3: Protein/peptide
Chitinase 2 /


Mass: 69740.609 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Yersinia entomophaga (bacteria) / References: UniProt: B6A879, chitinase

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Yersinia entomophaga toxin complex subunit A (YenTcA) in the pre-pore form
Type: COMPLEX / Entity ID: 1, 2, 3 / Source: NATURAL
Molecular weightValue: 2.08 MDa
Source (natural)Organism: Yersinia entomophaga (bacteria) / Strain: MH96
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 80 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

EM software

Name: EMAN / Version: 2.2

IDCategoryDetails
1particle selectionparticle picking was done in e2boxer.py using the SWARM algorithm
4CTF correctione2ctf.py was used to estiamte the CTF. CTF correction was performed as part of the e2refine.py routine
10initial Euler assignment
11final Euler assignment
133D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 19713
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9856 / Symmetry type: POINT

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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