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- EMDB-64507: Cryo-EM structure of the maize CER6-GL2 complex (inactive C222A m... -

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Basic information

Entry
Database: EMDB / ID: EMD-64507
TitleCryo-EM structure of the maize CER6-GL2 complex (inactive C222A mutant) in the presence of 28:0 CoA
Map datamain map
Sample
  • Complex: Cryo-EM structure of the maize CER6-GL2 complex (inactive C222A mutant) in the presence of 28:0 CoA
    • Protein or peptide: GL2
    • Protein or peptide: CER6
KeywordsComplex / inactive C222A mutant / 28:CoA / PLANT PROTEIN
Function / homology
Function and homology information


fatty acid elongase activity / acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / fatty acid biosynthetic process / membrane
Similarity search - Function
Very-long-chain 3-ketoacyl-CoA synthase / FAE1/Type III polyketide synthase-like protein / FAE1/Type III polyketide synthase-like protein / : / Transferase family / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal / Chloramphenicol acetyltransferase-like domain superfamily / Thiolase-like
Similarity search - Domain/homology
Protein ECERIFERUM 26-like / 3-ketoacyl-CoA synthase
Similarity search - Component
Biological speciesZea mays (maize)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsLiu Y / Zhang P
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32230050 China
CitationJournal: Sci Adv / Year: 2025
Title: Molecular basis of very-long-chain fatty acid elongation by the CER6-GL2 enzyme complex in plant wax biosynthesis.
Authors: Yaqi Liu / Yuan Chen / Xue Zhang / Mengxue Li / Ji Wang / Zhao Yang / Miaolian Ma / Zhiwei Zhao / Hongtao Liu / Fang Yu / Peng Zhang /
Abstract: Plant cuticular waxes, crucial hydrophobic barriers, are primarily composed of aliphatics derived from very-long-chain fatty acids (VLCFAs; >C28) synthesized by the endoplasmic reticulum fatty acid ...Plant cuticular waxes, crucial hydrophobic barriers, are primarily composed of aliphatics derived from very-long-chain fatty acids (VLCFAs; >C28) synthesized by the endoplasmic reticulum fatty acid elongase complex. The core catalytic subunit, CER6 (KCS6), requires interaction with the BAHD protein GL2 to elongate acyl chains beyond C28. We determined the cryo-electron microscopy structure of the maize CER6-GL2 (ZmCER6-ZmGL2) heterotetramer bound to coenzyme A (CoA) and malonyl-CoA, revealing a membrane-anchored ZmCER6 homodimer, with each cytosolic catalytic domain having a substrate tunnel. Structural and biochemical analyses suggest that ZmGL2's amino terminus binds ZmCER6 and remodels its substrate tunnel into a continuous hydrophobic channel at their interface, enabling acyl-chain elongation. CER6 uses a distinct Cys-His-Asn catalytic triad, differing from the histidine-dependent catalysis of mammalian elongases. GL2 acts noncatalytically to modulate CER6 activity. Comparative analyses suggest that species-specific substrate preferences arise from divergent CER2/GL2 interactions. This work elucidates the acyl-chain elongation mechanism of plant VLCFA biosynthesis and provides a foundation for engineering stress-resilient crops via wax modulation.
History
DepositionMay 5, 2025-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64507.png

Downloads & links

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Map

FileDownload / File: emd_64507.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 360 pix.
= 335.52 Å		0.93 Å/pix.
x 360 pix.
= 335.52 Å		0.93 Å/pix.
x 360 pix.
= 335.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.43
Minimum - Maximum-2.3460505 - 3.6794653
Average (Standard dev.)0.0033149787 (±0.07640257)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 335.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half A

Fileemd_64507_half_map_1.map
Annotationhalf A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half B

Fileemd_64507_half_map_2.map
Annotationhalf 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 : Cryo-EM structure of the maize CER6-GL2 complex (inactive C222A m...

EntireName: Cryo-EM structure of the maize CER6-GL2 complex (inactive C222A mutant) in the presence of 28:0 CoA
Components
  • Complex: Cryo-EM structure of the maize CER6-GL2 complex (inactive C222A mutant) in the presence of 28:0 CoA
    • Protein or peptide: GL2
    • Protein or peptide: CER6

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Supramolecule #1: Cryo-EM structure of the maize CER6-GL2 complex (inactive C222A m...

SupramoleculeName: Cryo-EM structure of the maize CER6-GL2 complex (inactive C222A mutant) in the presence of 28:0 CoA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Zea mays (maize)

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Macromolecule #1: GL2

MacromoleculeName: GL2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Zea mays (maize)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DYKDDDDKMV FEQHEEEAVA PGAVHGHRLS TVVPSSVTGE VDYALADADL AFKLHYLRGV YYYRSGDGLA TKVLKDPMFP WLDDHFPVAG RVRRAEAEGD GAPRRPYIKC NDCGVRIVEA RCDRDMAEWI RDAAPGRIRQ LCYDKVLGPE LFFSPLLYVQ ITNFKCGGLA ...String:
DYKDDDDKMV FEQHEEEAVA PGAVHGHRLS TVVPSSVTGE VDYALADADL AFKLHYLRGV YYYRSGDGLA TKVLKDPMFP WLDDHFPVAG RVRRAEAEGD GAPRRPYIKC NDCGVRIVEA RCDRDMAEWI RDAAPGRIRQ LCYDKVLGPE LFFSPLLYVQ ITNFKCGGLA LGFSWAHLIG DIPSAATCFN KWAQILSGKK PEATVLTPPN QPLQGQSPAA PRSVKQVGPM EDLWLVPAGR DMACYSFHVS DAVLKKLHQQ QNGRQDAAAG TFELVSALVW QAVAKIRGDV DTVTVVRADA AARSGKSLAN EMKVGYVESA GSSPAKTDVA ELAALLAKNV VDETAAVAAF QGDVLVYGGA NLTLVDMEQV DLYGLEIKGQ RPVYVEYGMD GVGDEGAVLV QPDADGRGRL VTVVLPGDEI DSLRAALGSA LHVA

UniProtKB: Protein ECERIFERUM 26-like

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Macromolecule #2: CER6

MacromoleculeName: CER6 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Zea mays (maize)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: HHHHHHMPSG GVFSGSVNLK HVKLGYQYLV NHFLTLLLVP VMAATALELA RLGPGELLSL WRSLELDLVH ILCSAFLVVF VGTVYVMSRP RPVYLVDYAC YKPPASCRVP FATFMEHTRL ISDDDKSVRF QTRILERSGL GEDTCLPPAN HYIPPNPSME ASRAEAQLVI ...String:
HHHHHHMPSG GVFSGSVNLK HVKLGYQYLV NHFLTLLLVP VMAATALELA RLGPGELLSL WRSLELDLVH ILCSAFLVVF VGTVYVMSRP RPVYLVDYAC YKPPASCRVP FATFMEHTRL ISDDDKSVRF QTRILERSGL GEDTCLPPAN HYIPPNPSME ASRAEAQLVI FSAIDDLVRR TGLKPKDIDI LVVNCSLFSP TPSLSAMIIN KYKLRSNIRS FNLSGMGASA GLISIDLARD MLQVHPNSNA LVVSTEIITP NFYQGSRRDM LLPNCLFRMG AAAILLSNRR REARRAKYRL VHVVRTHKGA DDRAYRCVYE EEDEQGFSGI SLSKELMAIA GDALKSNITT IGPLVLPMSE QLLFFFRLVG RKLVNKGWRP YIPDFKLAFE HFCIHAGGRA VIDELQKNLQ LSPRHVEASR MTLHRFGNTS SSSLWYELAY IEAKGRMRRG DRVWQIGFGS GFKCNSAVWK CLRSIKTPTN GPWDDCIHRY PVDVPEVVKL

UniProtKB: 3-ketoacyl-CoA synthase

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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

Concentration10 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 94244
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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