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- EMDB-15883: Mpf2Ba1 pore -

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Basic information

Entry
Database: EMDB / ID: EMD-15883
TitleMpf2Ba1 pore
Map dataCryoEM density of Mpf2Ba1 pore
Sample
  • Complex: Mpf2Ba1 21-mer pore
    • Protein or peptide: Mpf2Ba1
  • Ligand: MAGNESIUM ION
KeywordsPore-forming protein / pore / oligomer / insecticidal / pesticide / toxin
Function / homology
Function and homology information


metal ion binding / cytoplasm
Similarity search - Function
MACPF/perforin-like, beta-prism domain / MABP domain / MABP domain profile. / membrane-attack complex / perforin / MAC/Perforin domain / Membrane attack complex/perforin (MACPF) domain profile. / Membrane attack complex component/perforin (MACPF) domain
Similarity search - Domain/homology
MACPF domain-containing protein
Similarity search - Component
Biological speciesPseudomonas monteilii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 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 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15883.png

Downloads & links

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Map

FileDownload / File: emd_15883.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM density of Mpf2Ba1 pore
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 450 pix.
= 480.15 Å		1.07 Å/pix.
x 450 pix.
= 480.15 Å		1.07 Å/pix.
x 450 pix.
= 480.15 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.067 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.078
Minimum - Maximum-0.043810617 - 1.550782
Average (Standard dev.)0.0011804205 (±0.021977443)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 480.15002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Mpf2Ba1 pore halfmap B

Fileemd_15883_half_map_1.map
AnnotationMpf2Ba1 pore halfmap B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Mpf2Ba1 pore halfmap A

Fileemd_15883_half_map_2.map
AnnotationMpf2Ba1 pore halfmap A
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 21-mer pore

EntireName: Mpf2Ba1 21-mer pore
Components
  • Complex: Mpf2Ba1 21-mer pore
    • Protein or peptide: Mpf2Ba1
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Mpf2Ba1 21-mer pore

SupramoleculeName: Mpf2Ba1 21-mer 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: 21 / 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: 21 / 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

Concentration0.6 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 3.3000000000000003 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1413104
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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