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- EMDB-64505: Cryo-EM structure of the maize CER6-GL2 complex (inactive C222A m... -

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Basic information

Entry
Database: EMDB / ID: EMD-64505
TitleCryo-EM structure of the maize CER6-GL2 complex (inactive C222A mutant) bound with malonyl-CoA
Map datamain map
Sample
  • Complex: Cryo-EM structure of the maize CER6-GL2 complex (inactive C222A mutant) bound with malonyl-CoA
    • Protein or peptide: Protein ECERIFERUM 26-like
    • Protein or peptide: 3-ketoacyl-CoA synthase
  • Ligand: MALONYL-COENZYME A
KeywordsComplex / inactive C222A mutant / Malonyl-CoA / PLANT PROTEIN
Function / homology
Function and homology information


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: 2.96 Å
AuthorsLiu Y / Zhang P
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32230050 China
CitationJournal: To Be Published
Title: Molecular basis of very-long-chain fatty acid elongation by the CER6-GL2 enzyme complex in plant wax biosynthesis
Authors: Liu Y / Zhang P
History
DepositionMay 5, 2025-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64505.png

Downloads & links

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Map

FileDownload / File: emd_64505.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-2.473769 - 3.889357
Average (Standard dev.)0.0017234607 (±0.08485377)
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 B

Fileemd_64505_half_map_1.map
Annotationhalf B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half A

Fileemd_64505_half_map_2.map
Annotationhalf 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 : 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) bound with malonyl-CoA
Components
  • Complex: Cryo-EM structure of the maize CER6-GL2 complex (inactive C222A mutant) bound with malonyl-CoA
    • Protein or peptide: Protein ECERIFERUM 26-like
    • Protein or peptide: 3-ketoacyl-CoA synthase
  • Ligand: MALONYL-COENZYME A

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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) bound with malonyl-CoA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Zea mays (maize)

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Macromolecule #1: Protein ECERIFERUM 26-like

MacromoleculeName: Protein ECERIFERUM 26-like / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Zea mays (maize)
Molecular weightTheoretical: 46.86498 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DYKDDDDKMV FEQHEEEAVA PGAVHGHRLS TVVPSSVTGE VDYALADADL AFKLHYLRGV YYYRSGDGLA TKVLKDPMFP WLDDHFPVA GRVRRAEAEG DGAPRRPYIK CNDCGVRIVE ARCDRDMAEW IRDAAPGRIR QLCYDKVLGP ELFFSPLLYV Q ITNFKCGG ...String:
DYKDDDDKMV FEQHEEEAVA PGAVHGHRLS TVVPSSVTGE VDYALADADL AFKLHYLRGV YYYRSGDGLA TKVLKDPMFP WLDDHFPVA GRVRRAEAEG DGAPRRPYIK CNDCGVRIVE ARCDRDMAEW IRDAAPGRIR QLCYDKVLGP ELFFSPLLYV Q ITNFKCGG LALGFSWAHL IGDIPSAATC FNKWAQILSG KKPEATVLTP PNQPLQGQSP AAPRSVKQVG PMEDLWLVPA GR DMACYSF HVSDAVLKKL HQQQNGRQDA AAGTFELVSA LVWQAVAKIR GDVDTVTVVR ADAAARSGKS LANEMKVGYV ESA GSSPAK TDVAELAALL AKNVVDETAA VAAFQGDVLV YGGANLTLVD MEQVDLYGLE IKGQRPVYVE YGMDGVGDEG AVLV QPDAD GRGRLVTVVL PGDEIDSLRA ALGSALHVA

UniProtKB: Protein ECERIFERUM 26-like

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Macromolecule #2: 3-ketoacyl-CoA synthase

MacromoleculeName: 3-ketoacyl-CoA synthase / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
EC number: Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Source (natural)Organism: Zea mays (maize)
Molecular weightTheoretical: 56.381375 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: HHHHHHMPSG GVFSGSVNLK HVKLGYQYLV NHFLTLLLVP VMAATALELA RLGPGELLSL WRSLELDLVH ILCSAFLVVF VGTVYVMSR PRPVYLVDYA CYKPPASCRV PFATFMEHTR LISDDDKSVR FQTRILERSG LGEDTCLPPA NHYIPPNPSM E ASRAEAQL ...String:
HHHHHHMPSG GVFSGSVNLK HVKLGYQYLV NHFLTLLLVP VMAATALELA RLGPGELLSL WRSLELDLVH ILCSAFLVVF VGTVYVMSR PRPVYLVDYA CYKPPASCRV PFATFMEHTR LISDDDKSVR FQTRILERSG LGEDTCLPPA NHYIPPNPSM E ASRAEAQL VIFSAIDDLV RRTGLKPKDI DILVVNCSLF SPTPSLSAMI INKYKLRSNI RSFNLSGMGA SAGLISIDLA RD MLQVHPN SNALVVSTEI ITPNFYQGSR RDMLLPNCLF RMGAAAILLS NRRREARRAK YRLVHVVRTH KGADDRAYRC VYE EEDEQG FSGISLSKEL MAIAGDALKS NITTIGPLVL PMSEQLLFFF RLVGRKLVNK GWRPYIPDFK LAFEHFCIHA GGRA VIDEL QKNLQLSPRH VEASRMTLHR FGNTSSSSLW YELAYIEAKG RMRRGDRVWQ IGFGSGFKCN SAVWKCLRSI KTPTN GPWD DCIHRYPVDV PEVVKL

UniProtKB: 3-ketoacyl-CoA synthase

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Macromolecule #3: MALONYL-COENZYME A

MacromoleculeName: MALONYL-COENZYME A / type: ligand / ID: 3 / Number of copies: 2 / Formula: MLC
Molecular weightTheoretical: 853.58 Da
Chemical component information

ChemComp-MLC:
MALONYL-COENZYME A

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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: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 156994
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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