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- EMDB-36239: Cryo-EM sturcutre of DANGEROUS MIX 3 (DM3) from Hohenlieth (Hh-0) -

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Basic information

Entry
Database: EMDB / ID: EMD-36239
TitleCryo-EM sturcutre of DANGEROUS MIX 3 (DM3) from Hohenlieth (Hh-0)
Map data
Sample
  • Complex: DANGGEROUS MIX 3 (DM3) from Hohenlieth accession (Hh-0)
    • Protein or peptide: DM3Hh0
KeywordsHydrolase / Complex / Polymorphism / Hybrid necrosis
Function / homology: / Peptidase S33 / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / peptidase activity / Alpha/Beta hydrolase fold / proteolysis / DM3Hh0
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.89 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_36239.png

Downloads & links

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Map

FileDownload / File: emd_36239.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 271.68 Å		0.85 Å/pix.
x 320 pix.
= 271.68 Å		0.85 Å/pix.
x 320 pix.
= 271.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.849 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00965
Minimum - Maximum-0.012370641 - 0.04412158
Average (Standard dev.)-0.00017284714 (±0.0018378752)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 271.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36239_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_36239_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 : DANGGEROUS MIX 3 (DM3) from Hohenlieth accession (Hh-0)

EntireName: DANGGEROUS MIX 3 (DM3) from Hohenlieth accession (Hh-0)
Components
  • Complex: DANGGEROUS MIX 3 (DM3) from Hohenlieth accession (Hh-0)
    • Protein or peptide: DM3Hh0

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Supramolecule #1: DANGGEROUS MIX 3 (DM3) from Hohenlieth accession (Hh-0)

SupramoleculeName: DANGGEROUS MIX 3 (DM3) from Hohenlieth accession (Hh-0)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: DM3Hh0

MacromoleculeName: DM3Hh0 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 50.41475 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EHVTGKWFSV PELRLRDHRF IVPLDYSKSS PKITVFAREI VAVGKEEQAM PYLLYLQGGP GFEGPRPSEA SGWIQRACEE FRVVLLDQR GTGLSTPLIC SSMLQFKSAK ELADYLVHFR ADNIVKDAEF IRVRLVPKAD PWTILGQSFG GFCALTYLSF A PEGLKQVL ...String:
EHVTGKWFSV PELRLRDHRF IVPLDYSKSS PKITVFAREI VAVGKEEQAM PYLLYLQGGP GFEGPRPSEA SGWIQRACEE FRVVLLDQR GTGLSTPLIC SSMLQFKSAK ELADYLVHFR ADNIVKDAEF IRVRLVPKAD PWTILGQSFG GFCALTYLSF A PEGLKQVL ITGGIPPIGK ACTADDVYEA GFEQVARQNE KYYKRFPQDI EIVRELVNYL AESEGGGVPL PSGGILTPKG LQ TLGLSGL GSSTGFERLH YMLERVWDPI LVTGAPKCIS QFFLNAFESW HSFDANPLYA LLHEAIYCEG ASSGWSAHRL RDK YEYKFD AMKAVKESQP VLFTGEMIFP WMFDEIHALK PFKAAADLLA KKEDWPPLYD VPRLQNNKVP VAAAVYYEDM YVNF KLVTE TASHISGIRL WVTNEFMHSG LRDAGRQIID HLLGMINGKK PLF

UniProtKB: DM3Hh0

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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

Concentration0.17 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
100.0 mMNaClsodium choloride
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: The grid treated by graphene oxide prior to use
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Average electron dose: 49.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.9 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 413056
Initial angle assignmentType: OTHER / Details: Relion initial model
Final angle assignmentType: ANGULAR RECONSTITUTION / Details: Relion 3D refinement
FSC plot (resolution estimation)

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