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- PDB-22of: Cryo-EM structure of CeTECR-CeHACD complex -

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Basic information

Entry
Database: PDB / ID: 22of
TitleCryo-EM structure of CeTECR-CeHACD complex
Components
  • Probable very-long-chain enoyl-CoA reductase art-1
  • Very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase hpo-8
KeywordsMEMBRANE PROTEIN / very long chain fatty acids / TECR / HACD
Function / homology
Function and homology information


very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase / very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase activity / Synthesis of very long-chain fatty acyl-CoAs / very-long-chain enoyl-CoA reductase / very-long-chain enoyl-CoA reductase activity / very long-chain fatty acid biosynthetic process / 3-hydroxyacyl-CoA dehydratase activity / sphingolipid metabolic process / sphingolipid biosynthetic process / fatty acid elongation ...very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase / very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase activity / Synthesis of very long-chain fatty acyl-CoAs / very-long-chain enoyl-CoA reductase / very-long-chain enoyl-CoA reductase activity / very long-chain fatty acid biosynthetic process / 3-hydroxyacyl-CoA dehydratase activity / sphingolipid metabolic process / sphingolipid biosynthetic process / fatty acid elongation / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Protein-tyrosine phosphatase-like, PTPLA / Protein tyrosine phosphatase-like protein, PTPLA / : / TECR, ubiquitin-like domain / 3-oxo-5-alpha-steroid 4-dehydrogenase, C-terminal / 3-oxo-5-alpha-steroid 4-dehydrogenase/very-long-chain enoyl-CoA reductase / 3-oxo-5-alpha-steroid 4-dehydrogenase / Steroid 5-alpha reductase C-terminal domain profile. / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Chem-NDP / Very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase hpo-8 / Probable very-long-chain enoyl-CoA reductase art-1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsYu, L.Y. / Ren, R.B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of nematode TECR and HACD complex
Authors: Yu, L.Y. / Ren, R.B.
History
DepositionJan 18, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data 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: Probable very-long-chain enoyl-CoA reductase art-1
B: Very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase hpo-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3493
Polymers62,6032
Non-polymers7451
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 Probable very-long-chain enoyl-CoA reductase art-1


Mass: 35280.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: art-1, C15F1.6 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9N5Y2, very-long-chain enoyl-CoA reductase
#2: Protein Very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase hpo-8 / Probable 3-hydroxyacyl-CoA dehydratase


Mass: 27322.193 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: His tag: 2-11 linker:12-13 Drice cutting site:14-18 linker:19-23 Ce-HACD:24-241
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: hpo-8, T15B7.2 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O17040, very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: Nematode TECR-HACD complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Cell: sf9
Buffer solutionpH: 7.5
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: 2000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 52.76 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
12cryoSPARC3D reconstruction
13PHENIX1.20.1_4487model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 131428 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementHighest resolution: 3.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0184410
ELECTRON MICROSCOPYf_angle_d1.0466009
ELECTRON MICROSCOPYf_dihedral_angle_d5.874588
ELECTRON MICROSCOPYf_chiral_restr0.042672
ELECTRON MICROSCOPYf_plane_restr0.007736

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