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- EMDB-65115: Structure of plant diacylglycerol O-acyltransferase 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-65115
TitleStructure of plant diacylglycerol O-acyltransferase 1
Map data
Sample
  • Complex: Dimer of plant diacylglycerol O-acyltransferase 1 mutant with TAG and FFA
    • Protein or peptide: Diacylglycerol O-acyltransferase 1
  • Ligand: OLEIC ACID
  • Ligand: 2,3-bis[[(Z)-octadec-9-enoyl]oxy]propyl (Z)-octadec-9-enoate
KeywordsTAG synthysis / activity regulation / FFA / intramembrane enzyme / MEMBRANE PROTEIN
Function / homology
Function and homology information


positive regulation of seed germination / triglyceride biosynthetic process / diacylglycerol O-acyltransferase / diacylglycerol O-acyltransferase activity / chloroplast membrane / regulation of seed germination / glycerol metabolic process / embryo development ending in seed dormancy / response to abscisic acid / chloroplast envelope ...positive regulation of seed germination / triglyceride biosynthetic process / diacylglycerol O-acyltransferase / diacylglycerol O-acyltransferase activity / chloroplast membrane / regulation of seed germination / glycerol metabolic process / embryo development ending in seed dormancy / response to abscisic acid / chloroplast envelope / regulation of embryonic development / response to glucose / response to salt stress / lipid droplet / response to cold / carbohydrate metabolic process / endoplasmic reticulum membrane / membrane
Similarity search - Function
Diacylglycerol O-acyltransferase 1 / Sterol O-acyltransferase, ACAT/DAG/ARE types / Membrane bound O-acyl transferase, MBOAT / MBOAT, membrane-bound O-acyltransferase family
Similarity search - Domain/homology
Diacylglycerol O-acyltransferase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsLiu XY / Li JJ / Song DF / Liu ZF
Funding support China, 5 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32000852 China
National Natural Science Foundation of China (NSFC)31925024 China
Chinese Academy of SciencesYSBR-015 China
Chinese Academy of SciencesXDB37020101 China
Chinese Academy of SciencesZDBS-LY-SM003 China
CitationJournal: Plant Cell / Year: 2025
Title: Structural mechanisms underlying the free fatty acid-mediated regulation of DIACYLGLYCEROL O-ACYLTRANSFERASE 1 in Arabidopsis.
Authors: Xiuying Liu / Junjie Li / Danfeng Song / Zhenfeng Liu /
Abstract: Triacylglycerol (TAG) constitutes the primary component of plant oils and is essential for food and biodiesel production. Diacylglycerol O-acyltransferase-1 (DGAT1), the key rate-limiting enzyme in ...Triacylglycerol (TAG) constitutes the primary component of plant oils and is essential for food and biodiesel production. Diacylglycerol O-acyltransferase-1 (DGAT1), the key rate-limiting enzyme in TAG biosynthesis, is an important target for engineering plants with enhanced oil yield and improved fatty acyl composition. Environmental stress triggers the accumulation of toxic lipid intermediates such as free fatty acids (FFAs) and diacylglycerols (DAGs). Plants alleviate lipid toxicity by upregulating DGAT1 to channel the intermediates into TAG. Through biochemical studies, we demonstrate that FFAs directly enhance the activity of Arabidopsis (Arabidopsis thaliana) DGAT1 (AtDGAT1) by ∼3-fold. Cryo-electron microscopy structures of wild-type (WT) AtDGAT1 and a low-activity mutant (H447A) reveal the binding sites for both substrates (DAG and oleoyl-CoA), 2 products (TAG and CoASH), and multiple FFA molecules. Remarkably, mutating a cysteine residue (Cys246) in contact with the FFA head group to Ala, Ser, or Thr increases AtDAGT1 activity significantly. The C246A mutant accommodates the carboxyl group of FFA slightly deeper within the active site, potentially enhancing substrate binding. Furthermore, the FFA molecules orient the acyl-CoA tail at a position favorable for the catalytic reaction. Our integrated biochemical and structural results provide insights into the catalytic mechanism and activity regulation of DGAT1, which will enable the future engineering of oil crops.
History
DepositionJun 21, 2025-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65115.png

Downloads & links

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Map

FileDownload / File: emd_65115.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.56
Minimum - Maximum-6.3009825 - 7.095996
Average (Standard dev.)-0.002723408 (±0.11016851)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65115_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65115_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Dimer of plant diacylglycerol O-acyltransferase 1 mutant with TAG...

EntireName: Dimer of plant diacylglycerol O-acyltransferase 1 mutant with TAG and FFA
Components
  • Complex: Dimer of plant diacylglycerol O-acyltransferase 1 mutant with TAG and FFA
    • Protein or peptide: Diacylglycerol O-acyltransferase 1
  • Ligand: OLEIC ACID
  • Ligand: 2,3-bis[[(Z)-octadec-9-enoyl]oxy]propyl (Z)-octadec-9-enoate

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Supramolecule #1: Dimer of plant diacylglycerol O-acyltransferase 1 mutant with TAG...

SupramoleculeName: Dimer of plant diacylglycerol O-acyltransferase 1 mutant with TAG and FFA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 120 KDa

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Macromolecule #1: Diacylglycerol O-acyltransferase 1

MacromoleculeName: Diacylglycerol O-acyltransferase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: diacylglycerol O-acyltransferase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 59.997629 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MAILDSAGVT TVTENGGGEF VDLDRLRRRK SRSDSSNGLL LSGSDNNSPS DDVGAPADVR DRIDSVVNDD AQGTANLAGD NNGGGDNNG GGRGGGEGRG NADATFTYRP SVPAHRRARE SPLSSDAIFK QSHAGLFNLC VVVLIAVNSR LIIENLMKYG W LIRTDFWF ...String:
MAILDSAGVT TVTENGGGEF VDLDRLRRRK SRSDSSNGLL LSGSDNNSPS DDVGAPADVR DRIDSVVNDD AQGTANLAGD NNGGGDNNG GGRGGGEGRG NADATFTYRP SVPAHRRARE SPLSSDAIFK QSHAGLFNLC VVVLIAVNSR LIIENLMKYG W LIRTDFWF SSRSLRDWPL FMCCISLSIF PLAAFTVEKL VLQKYISEPV VIFLHIIITM TEVLYPVYVT LRCDSAFLSG VT LMLLTAI VWLKLVSYAH TSYDIRSLAN AADKANPEVS YYVSLKSLAY FMVAPTLCYQ PSYPRSACIR KGWVARQFAK LVI FTGFMG FIIEQYINPI VRNSKHPLKG DLLYAIERVL KLSVPNLYVW LCMFYCFFHL WLNILAELLC FGDREFYKDW WNAK SVGDY WRMWNMPVHK WMVRHIYFPC LRSKIPKTLA IIIAFLVSAV FHELCIAVPC RLFKLWAFLG IMFQVPLVFI TNYLQ ERFG STVGNMIFWF IFCIFGQPMC VLLYYHDLMN RKGSMSGPHH HHHH

UniProtKB: Diacylglycerol O-acyltransferase 1

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Macromolecule #2: OLEIC ACID

MacromoleculeName: OLEIC ACID / type: ligand / ID: 2 / Number of copies: 2 / Formula: OLA
Molecular weightTheoretical: 282.461 Da
Chemical component information

ChemComp-OLA:
OLEIC ACID

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Macromolecule #3: 2,3-bis[[(Z)-octadec-9-enoyl]oxy]propyl (Z)-octadec-9-enoate

MacromoleculeName: 2,3-bis[[(Z)-octadec-9-enoyl]oxy]propyl (Z)-octadec-9-enoate
type: ligand / ID: 3 / Number of copies: 2 / Formula: A1LVF
Molecular weightTheoretical: 885.432 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

Concentration6 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2879867
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. V3.1) / Number images used: 224579
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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