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- EMDB-63076: Cryo-EM structure of CsKCS6-CsCER2 like1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-63076
TitleCryo-EM structure of CsKCS6-CsCER2 like1 complex
Map data
Sample
  • Complex: CsKCS2-CsCER2 like1 complex
    • Protein or peptide: CsCER2 like1
    • Protein or peptide: 3-ketoacyl-CoA synthase
  • Ligand: DODECANE
  • Ligand: HEXADECANE
KeywordsCsKCS6-CsCER2 like1 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: 2.4 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
DepositionJan 10, 2025-
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_63076.png

Downloads & links

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Map

FileDownload / File: emd_63076.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 360 pix.
= 296.64 Å		0.82 Å/pix.
x 360 pix.
= 296.64 Å		0.82 Å/pix.
x 360 pix.
= 296.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-2.3294196 - 3.9008553
Average (Standard dev.)-0.00019164743 (±0.08757274)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 296.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63076_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_63076_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 : CsKCS2-CsCER2 like1 complex

EntireName: CsKCS2-CsCER2 like1 complex
Components
  • Complex: CsKCS2-CsCER2 like1 complex
    • Protein or peptide: CsCER2 like1
    • Protein or peptide: 3-ketoacyl-CoA synthase
  • Ligand: DODECANE
  • Ligand: HEXADECANE

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Supramolecule #1: CsKCS2-CsCER2 like1 complex

SupramoleculeName: CsKCS2-CsCER2 like1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Citrus sinensis (sweet orange)

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Macromolecule #1: CsCER2 like1

MacromoleculeName: CsCER2 like1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Citrus sinensis (sweet orange)
Molecular weightTheoretical: 50.863973 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASWSHPQFE KGGGARGGSG GGSWSHPQFE KGSMVNDLLI HSIRLSSVGP GKATGSDVVH ELSGMDLAMK LHYLKGFYIF RSHAVQGLS VKLIKESTFY LFNNYYWTCA RLRRSDSGRP YLKCNDCGAR FVEAQCDKTV DELLEMGDYS SFPNLLVYHQ P IGPDLAFS ...String:
MASWSHPQFE KGGGARGGSG GGSWSHPQFE KGSMVNDLLI HSIRLSSVGP GKATGSDVVH ELSGMDLAMK LHYLKGFYIF RSHAVQGLS VKLIKESTFY LFNNYYWTCA RLRRSDSGRP YLKCNDCGAR FVEAQCDKTV DELLEMGDYS SFPNLLVYHQ P IGPDLAFS PPIYLQVTWF KCGGMSLGMS WAHILGDAFS ACEFINKMGQ VLTAIKANGP PTCAKSISPG KIVKLEMSSS FF KPKDPIS IKWVDPVGDH WVTANNSKMD TFSFHLTDSR ISHLQSNFRN HHQIPVFESL CAIIWQCVAK IRDGFGPNNV TIC KKGSHI RENGNLSNGQ IISAFQADFS VMEADLEKLA KVLCYEAVED ERSRIEETME KGNGVADYIV YGANLTFVNW EDAD VYGLE LNGEKADFAS FSIQGVGDEG AVLVLPGGKG RILKIILPED QILKLKTELK MNGVL

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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: Citrus sinensis (sweet orange)
Molecular weightTheoretical: 59.652207 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKG DYKDDDDKID YKDDDDKGSM PQTLPDFSNS VKLKYVKLGY QYLVNHILYL LLVPIMVAIL IEVLRLGPDE ILNLWKSLH FDLVQILCSS FLIIFIATVY FMSKPRHVYL VDYACYKPPV TCRVPFATFM EHSRLILKNN PKSVEFQMRI L ERSGLGEE ...String:
MDYKDDDDKG DYKDDDDKID YKDDDDKGSM PQTLPDFSNS VKLKYVKLGY QYLVNHILYL LLVPIMVAIL IEVLRLGPDE ILNLWKSLH FDLVQILCSS FLIIFIATVY FMSKPRHVYL VDYACYKPPV TCRVPFATFM EHSRLILKNN PKSVEFQMRI L ERSGLGEE TCLPPAIHYI PPTPTMEAAR GEAELVIFSA MDSLLQKTGL KPKDIDILIV NCSLFSPTPS LSAMVINKYK LR SNIKSFN LSGMGCSAGL ISIDLARDLL QVHPNSNAVV VSTEIITPNY YQGNERAMLL PNCLFRMGGA AILLSNRRRN RSR AKYRLV HVVRTHKGAD DKAYRCVFEE EDKEGKVGIS LSKDLMAIAG EALKSNITTI GPLVLPASEQ LLFLMTLIGR KIFN PKWKP YIPDFKQAFE HFCIHAGGRA VIDELQKNLQ LSAEQVEASR MTLHRFGNTS SSSLWYEMSY IEEKGRMKKG DRVWQ IAFG SGFKCNSAVW KCNKTIKTTT DNPWSDCIDR YPVHIPEIVK L

UniProtKB: 3-ketoacyl-CoA synthase

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Macromolecule #3: DODECANE

MacromoleculeName: DODECANE / type: ligand / ID: 3 / Number of copies: 1 / Formula: D12
Molecular weightTheoretical: 170.335 Da
Chemical component information

ChemComp-D12:
DODECANE

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Macromolecule #4: HEXADECANE

MacromoleculeName: HEXADECANE / type: ligand / ID: 4 / Number of copies: 1 / Formula: R16
Molecular weightTheoretical: 226.441 Da
Chemical component information

ChemComp-R16:
HEXADECANE

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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: 1.6 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 reconstructionResolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 272363
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING

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