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- EMDB-62504: Cryo-EM structure of CsKCS6-CsCER2 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-62504
TitleCryo-EM structure of CsKCS6-CsCER2 complex
Map data
Sample
  • Complex: CsKCS6-CER2 complex
    • Protein or peptide: 3-ketoacyl-CoA synthase
    • Protein or peptide: CsCER2
  • Ligand: DODECANE
KeywordsCsKCS6-CsCER2 complex / PLANT PROTEIN
Function / homology
Function and homology information


fatty acid elongase activity / 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 / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal / Thiolase-like
Similarity search - Domain/homology
3-ketoacyl-CoA synthase
Similarity search - Component
Biological speciesCitrus sinensis (sweet orange)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsWang Y / Guan ZY / Zhu F / Chen YJ / Yin P
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: structural basis for Synthesis of long-chain fatty acids
Authors: Wang Y / Yin P
History
DepositionNov 25, 2024-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62504.png

Downloads & links

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Map

FileDownload / File: emd_62504.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 280 pix.
= 299.6 Å		1.07 Å/pix.
x 280 pix.
= 299.6 Å		1.07 Å/pix.
x 280 pix.
= 299.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-3.0759628 - 4.904535
Average (Standard dev.)0.001884503 (±0.09009315)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 299.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_62504_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62504_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 : CsKCS6-CER2 complex

EntireName: CsKCS6-CER2 complex
Components
  • Complex: CsKCS6-CER2 complex
    • Protein or peptide: 3-ketoacyl-CoA synthase
    • Protein or peptide: CsCER2
  • Ligand: DODECANE

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Supramolecule #1: CsKCS6-CER2 complex

SupramoleculeName: CsKCS6-CER2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Citrus sinensis (sweet orange)

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Macromolecule #1: 3-ketoacyl-CoA synthase

MacromoleculeName: 3-ketoacyl-CoA synthase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
EC number: Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Source (natural)Organism: Citrus sinensis (sweet orange)
Molecular weightTheoretical: 47.769559 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: IFIATVYFMS KPRHVYLVDY ACYKPPVTCR VPFATFMEHS RLILKNNPKS VEFQMRILER SGLGEETCLP PAIHYIPPTP TMEAARGEA ELVIFSAMDS LLQKTGLKPK DIDILIVNCS LFSPTPSLSA MVINKYKLRS NIKSFNLSGM GCSAGLISID L ARDLLQVH ...String:
IFIATVYFMS KPRHVYLVDY ACYKPPVTCR VPFATFMEHS RLILKNNPKS VEFQMRILER SGLGEETCLP PAIHYIPPTP TMEAARGEA ELVIFSAMDS LLQKTGLKPK DIDILIVNCS LFSPTPSLSA MVINKYKLRS NIKSFNLSGM GCSAGLISID L ARDLLQVH PNSNAVVVST EIITPNYYQG NERAMLLPNC LFRMGGAAIL LSNRRRNRSR AKYRLVHVVR THKGADDKAY RC VFEEEDK EGKVGISLSK DLMAIAGEAL KSNITTIGPL VLPASEQLLF LMTLIGRKIF NPKWKPYIPD FKQAFEHFCI HAG GRAVID ELQKNLQLSA EQVEASRMTL HRFGNTSSSS LWYEMSYIEE KGRMKKGDRV WQIAFGSGFK CNSAVWKCNK TIKT TTDNP WSDCIDRYPV HIPEIVKL

UniProtKB: 3-ketoacyl-CoA synthase

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Macromolecule #2: CsCER2

MacromoleculeName: CsCER2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Citrus sinensis (sweet orange)
Molecular weightTheoretical: 48.156148 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NPENRVSGIK LSSVVPAKAT GNQDYELKNI DLAMKLHYIK GVYFFNREAV RGLTIFDLKR PMFQLLDIFY TASGRIRRPE TAGAGRPFI KCNDGGVRIV EAFCDDQTIA EWLAMDHESR DDCLAYGSEL GPDLAFSPLV FVQFTSFKCG GMSLGLSWAH V LGDPFSAS ...String:
NPENRVSGIK LSSVVPAKAT GNQDYELKNI DLAMKLHYIK GVYFFNREAV RGLTIFDLKR PMFQLLDIFY TASGRIRRPE TAGAGRPFI KCNDGGVRIV EAFCDDQTIA EWLAMDHESR DDCLAYGSEL GPDLAFSPLV FVQFTSFKCG GMSLGLSWAH V LGDPFSAS AFVSMWAQIM AGRVPPKSLH EPEPEKSETE TQTRASESVA GNLYPIKRVD PVGDHWQFPN NCNMKTHTFQ FT KKQLDQM ASNLRYRGIR EAAAVSHFEV ISATIWKLLA KASEDSGPGV VTICRYNGQR ENETASNDMV LSTAEVDFDV SKS DVWELS TLIADKRKDV DEKVLSESSD FIMYGANLTF VDMEEADVYG LKLQGQKPVD VNYSINGVGE QGVVLVLAGP EEDS GRGRD RGSTVTVVLP ENQLEKLMNE LNQEWNLA

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Macromolecule #3: DODECANE

MacromoleculeName: DODECANE / type: ligand / ID: 3 / Number of copies: 2 / Formula: D12
Molecular weightTheoretical: 170.335 Da
Chemical component information

ChemComp-D12:
DODECANE

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k 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: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 168801
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING

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