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- EMDB-36240: Cryo-EM structure of alpha/beta hydrolase DANGEROUS MIX 3 (DM3) f... -

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Basic information

Entry
Database: EMDB / ID: EMD-36240
TitleCryo-EM structure of alpha/beta hydrolase DANGEROUS MIX 3 (DM3) forms compartmentalized hexamer structure
Map data
Sample
  • Complex: Homohexamer complex of DM3 from Columbia accession (Col-0)
    • Protein or peptide: AT3g61540/F2A19_140
KeywordsComplex / immune related alpha/beta hydrolase / PROLYL AMINOPEPTIDASE 2 / HYDROLASE
Function / homology
Function and homology information


vacuole / aminopeptidase activity / proteolysis / cytosol
Similarity search - Function
: / Peptidase S33 / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsKim G / Song JJ
Funding support Korea, Republic Of, 1 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2020R1A2B5B03001517 Korea, Republic Of
CitationJournal: Mol.Cell / Year: 2025
Title: Structure determinants of DANGEROUS MIX 3, an alpha/beta hydrolase, for triggering NLR-mediated genetic incompatibility in plants
Authors: Kim G / Song JJ
History
DepositionMay 21, 2023-
Header (metadata) releaseDec 25, 2024-
Map releaseDec 25, 2024-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36240.png

Downloads & links

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Map

FileDownload / File: emd_36240.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 360 pix.
= 321.948 Å		0.89 Å/pix.
x 360 pix.
= 321.948 Å		0.89 Å/pix.
x 360 pix.
= 321.948 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8943 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.037
Minimum - Maximum-0.12128737 - 0.19400492
Average (Standard dev.)0.00021329698 (±0.008060645)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 321.948 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36240_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36240_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Homohexamer complex of DM3 from Columbia accession (Col-0)

EntireName: Homohexamer complex of DM3 from Columbia accession (Col-0)
Components
  • Complex: Homohexamer complex of DM3 from Columbia accession (Col-0)
    • Protein or peptide: AT3g61540/F2A19_140

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Supramolecule #1: Homohexamer complex of DM3 from Columbia accession (Col-0)

SupramoleculeName: Homohexamer complex of DM3 from Columbia accession (Col-0)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: AT3g61540/F2A19_140

MacromoleculeName: AT3g61540/F2A19_140 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 50.432719 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: EHVTGKWFSV PELRLRDHRF IVPLDYSKSS PKITVFAREI VAVGKEEQAM PYLLYLQGGP GFEGPRPSEA SGWIQRACEE FRVVLLDQR GTGLSTPLTC SSMLQFKSAK ELADYLVHFR ADNIVKDAEF IRVRLVPKAD PWTILGQSFG GFCALTYLSF A PEGLKQVL ...String:
EHVTGKWFSV PELRLRDHRF IVPLDYSKSS PKITVFAREI VAVGKEEQAM PYLLYLQGGP GFEGPRPSEA SGWIQRACEE FRVVLLDQR GTGLSTPLTC SSMLQFKSAK ELADYLVHFR ADNIVKDAEF IRVRLVPKAD PWTILGQSFG GFCALTYLSF A PEGLKQVL ITGGIPPIGK ACTADDVYEA GFEQVARQNE KYYKRFPQDI EIVRELVNYL AESEGGGVPL PSGGILTPKG LQ TLGLSGL GSSTGFERLH YMLERVWDPI LVTGAPKCIS QFFLNAFESW HSFDTNPLYA LLHEAIYCEG ASSGWSAHRL RDK YEYKFD AMKAVKESQP VLFTGEMIFP WMFDEIHALK PFKAAADLLA KKEDWPPLYD VPRLQNNKVP VAAAVYYEDM YVNF KLVTE TASHISGIRL WVTNEFMHSG LRDAGRQIID HLLGMINGKK PLF

UniProtKB: AT3g61540/F2A19_140

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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

Concentration0.2 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
100.0 mMNaClsodium chloride
50.0 mMTrisTrisamine
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
Details: After glow discharge, graphene oxide was treated onto the grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Made by SWISSMODELER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 330509
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Details: Relion initial model building
Final angle assignmentType: ANGULAR RECONSTITUTION / Details: Relion 3D refinement
FSC plot (resolution estimation)

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