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- EMDB-15882: Mp2Ba1 pre-pore -

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Basic information

Entry
Database: EMDB / ID: EMD-15882
TitleMp2Ba1 pre-pore
Map dataCryoEM density of Mpf2Ba1 pre-pore
Sample
  • Complex: Mpf2Ba1 22-mer pre-pore
    • Protein or peptide: Mpf2Ba1
  • Ligand: MAGNESIUM ION
KeywordsPore-forming protein / oligomer / pre-pore / MACPF / insecticidal / pesticide / TOXIN
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)
Methodsingle 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 JZ / Sethi A / Kassa A / Crane V / Lu A / Nelson ME / Eswar N / Topf M / Saibil HR
Funding support United Kingdom, 2 items
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, 2022-
Header (metadata) releaseMay 31, 2023-
Map releaseMay 31, 2023-
UpdateJul 26, 2023-
Current statusJul 26, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15882.png

Downloads & links

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Map

FileDownload / File: emd_15882.map.gz / Format: CCP4 / Size: 83.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM density of Mpf2Ba1 pre-pore
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 128 pix.
= 134.4 Å		1.05 Å/pix.
x 450 pix.
= 472.5 Å		1.05 Å/pix.
x 379 pix.
= 397.95 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0813
Minimum - Maximum-0.001961096 - 1.8143613
Average (Standard dev.)0.008070427 (±0.06687475)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin017225
Dimensions450379128
Spacing379450128
CellA: 397.94998 Å / B: 472.49997 Å / C: 134.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Mpf2Ba1 pre-pore halfmap A

Fileemd_15882_half_map_1.map
AnnotationMpf2Ba1 pre-pore halfmap A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Mpf2Ba1 pre-pore halfmap B

Fileemd_15882_half_map_2.map
AnnotationMpf2Ba1 pre-pore halfmap B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mpf2Ba1 22-mer pre-pore

EntireName: Mpf2Ba1 22-mer pre-pore
Components
  • Complex: Mpf2Ba1 22-mer pre-pore
    • Protein or peptide: Mpf2Ba1
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Mpf2Ba1 22-mer pre-pore

SupramoleculeName: Mpf2Ba1 22-mer pre-pore / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Pseudomonas monteilii (bacteria)

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Macromolecule #1: Mpf2Ba1

MacromoleculeName: Mpf2Ba1 / type: protein_or_peptide / ID: 1 / Number of copies: 22 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas monteilii (bacteria)
Molecular weightTheoretical: 49.961504 KDa
SequenceString: TVLPGVEAIG LGYNPFISYA SVNSGAVQLF DWATAKKREV PFKAGYFVPE IVDVQQNDSA TYTNVSGNTI SEYQRSLATS VAIEGRYNF FSGSLSTDFD SNSLRNAENE FTRIQQSINL WSLRLPSVKS LRELMLPHMR QQLDELNVND PKAISRYFDR V GSHFLTGI ...String:
TVLPGVEAIG LGYNPFISYA SVNSGAVQLF DWATAKKREV PFKAGYFVPE IVDVQQNDSA TYTNVSGNTI SEYQRSLATS VAIEGRYNF FSGSLSTDFD SNSLRNAENE FTRIQQSINL WSLRLPSVKS LRELMLPHMR QQLDELNVND PKAISRYFDR V GSHFLTGI VMGGRAILAS STNKLRVKRD YSVSVVAKAS YEGLTGQLSA EAKAKYGESI SSFTQYSNTH QEVRGGDGAK AH GVFSGKK EDFQAWVDSV SASPDFVDFV PTIPMQEIWT LCSSEAQAEA MRKHYDDVWA PAQSEKYRVK ANYIDQLVVI TGG SSTIEP PVGYSKIEYD LNAGAGGDFI YLCYHEQTWQ ADRPKDAVTD IRIIFNKEPT PPGYTKLPQD LNKGAGGDDV FLCY KTEAY NTDTAINKVT VIGGNNADIN APYGYLKVPG DLNRGAGGNF IYACTFVGK

UniProtKB: MACPF domain-containing protein

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 22 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 64248

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