[English] 日本語
Yorodumi
- PDB-8b6v: Mp2Ba1 pre-pore -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8b6v
TitleMp2Ba1 pre-pore
ComponentsMpf2Ba1
KeywordsTOXIN / Pore-forming protein / oligomer / pre-pore / MACPF / insecticidal / pesticide
Function / homologyMABP domain / MABP domain profile. / membrane-attack complex / perforin / Membrane attack complex/perforin (MACPF) domain profile. / MAC/Perforin domain / Membrane attack complex component/perforin (MACPF) domain / cytoplasm / MACPF domain-containing protein
Function and homology information
Biological speciesPseudomonas monteilii (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsMarini, G. / Poland, B. / Leininger, C. / Lukoyanova, N. / Spielbauer, D. / Barry, J. / Altier, D. / Lum, A. / Scolaro, E. / Perez Ortega, C. ...Marini, G. / Poland, B. / Leininger, C. / Lukoyanova, N. / Spielbauer, D. / Barry, J. / Altier, D. / Lum, A. / Scolaro, E. / Perez Ortega, C. / Yalpani, N. / Sandahl, G. / Mabry, T. / Klever, J. / Nowatzki, T. / Zhao, J.Z. / Sethi, A. / Kassa, A. / Crane, V. / Lu, A. / Nelson, M.E. / Eswar, N. / Topf, M. / Saibil, H.R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust202679/Z/16/Z United Kingdom
Wellcome Trust206166/Z/17/Z United Kingdom
CitationJournal: Nat Commun / Year: 2023
Title: Structural journey of an insecticidal protein against western corn rootworm.
Authors: Guendalina Marini / Brad Poland / Chris Leininger / Natalya Lukoyanova / Dan Spielbauer / Jennifer K Barry / Dan Altier / Amy Lum / Eric Scolaro / Claudia Pérez Ortega / Nasser Yalpani / ...Authors: Guendalina Marini / Brad Poland / Chris Leininger / Natalya Lukoyanova / Dan Spielbauer / Jennifer K Barry / Dan Altier / Amy Lum / Eric Scolaro / Claudia Pérez Ortega / Nasser Yalpani / Gary Sandahl / Tim Mabry / Jeffrey Klever / Timothy Nowatzki / Jian-Zhou Zhao / Amit Sethi / Adane Kassa / Virginia Crane / Albert L Lu / Mark E Nelson / Narayanan Eswar / Maya Topf / Helen R Saibil /
Abstract: The broad adoption of transgenic crops has revolutionized agriculture. However, resistance to insecticidal proteins by agricultural pests poses a continuous challenge to maintaining crop productivity ...The broad adoption of transgenic crops has revolutionized agriculture. However, resistance to insecticidal proteins by agricultural pests poses a continuous challenge to maintaining crop productivity and new proteins are urgently needed to replace those utilized for existing transgenic traits. We identified an insecticidal membrane attack complex/perforin (MACPF) protein, Mpf2Ba1, with strong activity against the devastating coleopteran pest western corn rootworm (WCR) and a novel site of action. Using an integrative structural biology approach, we determined monomeric, pre-pore and pore structures, revealing changes between structural states at high resolution. We discovered an assembly inhibition mechanism, a molecular switch that activates pre-pore oligomerization upon gut fluid incubation and solved the highest resolution MACPF pore structure to-date. Our findings demonstrate not only the utility of Mpf2Ba1 in the development of biotechnology solutions for protecting maize from WCR to promote food security, but also uncover previously unknown mechanistic principles of bacterial MACPF assembly.
History
DepositionSep 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mpf2Ba1
C: Mpf2Ba1
D: Mpf2Ba1
E: Mpf2Ba1
F: Mpf2Ba1
G: Mpf2Ba1
H: Mpf2Ba1
I: Mpf2Ba1
J: Mpf2Ba1
K: Mpf2Ba1
L: Mpf2Ba1
M: Mpf2Ba1
N: Mpf2Ba1
O: Mpf2Ba1
P: Mpf2Ba1
Q: Mpf2Ba1
R: Mpf2Ba1
S: Mpf2Ba1
T: Mpf2Ba1
U: Mpf2Ba1
V: Mpf2Ba1
W: Mpf2Ba1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,099,68844
Polymers1,099,15322
Non-polymers53522
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area94910 Å2
ΔGint-40 kcal/mol
Surface area362400 Å2

-
Components

#1: Protein ...
Mpf2Ba1


Mass: 49961.504 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Source: (natural) Pseudomonas monteilii (bacteria) / References: UniProt: A0A4Y8SM08
#2: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Mpf2Ba1 22-mer pre-pore / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Pseudomonas monteilii (bacteria)
Buffer solutionpH: 7.4
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: OTHER / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 64248 / 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