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- PDB-9lgy: Cryo-EM structure of CsKCS6-CsCER2 like1 complex -

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Basic information

Entry
Database: PDB / ID: 9lgy
TitleCryo-EM structure of CsKCS6-CsCER2 like1 complex
Components
  • 3-ketoacyl-CoA synthase
  • CsCER2 like1
KeywordsPLANT PROTEIN / CsKCS6-CsCER2 like1 complex
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
DODECANE / HEXADECANE / 3-ketoacyl-CoA synthase
Similarity search - Component
Biological speciesCitrus sinensis (sweet orange)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsWang, Y. / Guan, Z.Y. / Zhu, F. / Chen, Y.J. / Yin, P.
Funding support China, 1items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CsCER2 like1
C: CsCER2 like1
B: 3-ketoacyl-CoA synthase
E: 3-ketoacyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,4296
Polymers221,0324
Non-polymers3972
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein CsCER2 like1


Mass: 50863.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrus sinensis (sweet orange) / Production host: Homo sapiens (human)
#2: Protein 3-ketoacyl-CoA synthase


Mass: 59652.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrus sinensis (sweet orange) / Gene: CISIN_1g011007mg / Production host: Homo sapiens (human)
References: UniProt: A0A067FRD2, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#3: Chemical ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26
#4: Chemical ChemComp-R16 / HEXADECANE


Mass: 226.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CsKCS2-CsCER2 like1 complex / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Source (natural)Organism: Citrus sinensis (sweet orange)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 272363 / Symmetry type: POINT
RefinementHighest resolution: 2.4 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00312596
ELECTRON MICROSCOPYf_angle_d0.51217010
ELECTRON MICROSCOPYf_dihedral_angle_d5.741707
ELECTRON MICROSCOPYf_chiral_restr0.0431897
ELECTRON MICROSCOPYf_plane_restr0.0042160

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