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- PDB-9x0f: Cryo-EM structure of EvSS -

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Basic information

Entry
Database: PDB / ID: 9x0f
TitleCryo-EM structure of EvSS
ComponentsStellatatriene synthase
KeywordsBIOSYNTHETIC PROTEIN / Stellatatriene synthase
Function / homology
Function and homology information


stellata-2,6,19-triene synthase / alcohol biosynthetic process / mycotoxin biosynthetic process / Transferases; Transferring alkyl or aryl groups, other than methyl groups / prenyltransferase activity / terpenoid biosynthetic process / lyase activity / metal ion binding
Similarity search - Function
Terpene synthase family 2, C-terminal metal binding / Polyprenyl synthases signature 1. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
Stellatatriene synthase
Similarity search - Component
Biological speciesAspergillus stellatus (mold)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsBai, L. / Lyu, R.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J Am Chem Soc / Year: 2026
Title: Structural Insights into Three Bifunctional Sesterterpene Synthases and Product Profile Investigation by Domain Swapping and Active Site Mutation.
Authors: Zhenyu Lei / Ruiqing Lyu / Wenlong Song / Chenyu Zhang / Lin Bai / Donghui Yang / Ming Ma /
Abstract: Terpene synthases (TSs) catalyze the formation of diverse hydrocarbon skeletons by using different linear polyisoprenyl diphosphates as the substrates, whose biosyntheses are catalyzed by ...Terpene synthases (TSs) catalyze the formation of diverse hydrocarbon skeletons by using different linear polyisoprenyl diphosphates as the substrates, whose biosyntheses are catalyzed by prenyltransferases (PTs). In nature, some TSs are bifunctional enzymes catalyzing both polyisoprenyl diphosphate formation and subsequent cyclization, containing a C-terminal PT domain and an N-terminal terpene cyclase (TC) domain. To date, several bifunctional PT-TC diterpene synthases and triterpene synthase have been structurally characterized, whereas there have been no structural insights reported for bifunctional PT-TC sesterterpene synthases (StTSs). We here report the cryo-EM structures of three full-length StTSs (EvAS, EvSS, and PbSS), revealing that EvAS and PbSS share a similar PT-driven hexamerization architecture, but EvSS possesses a PT-hexamer stacked helical hollow tubular architecture that has not been observed for other TSs. Domain swapping among the three StTSs shows that not only the production yields but also the major product types of TCs can be greatly affected by different noncovalently linked PTs. The atypical α-helical bundle crystal structure of the TC domain of EvAS was determined, revealing key secondary structures whose positions may affect the cyclization function. Systematic mutations on key residues in the active sites of the TC domains of EvAS and EvSS generated seven new compounds, expanding the structural diversity of sesterterpenes. These results uncover the new structural architecture of bifunctional TSs and expand our understanding of their substrate transfer and catalytic function, and benefit the rational engineering and design of collaborated PT and TC pairs in the generation of terpene molecules.
History
DepositionSep 30, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 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

Downloads & links

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Assembly

Deposited unit
A: Stellatatriene synthase
B: Stellatatriene synthase
C: Stellatatriene synthase
D: Stellatatriene synthase
E: Stellatatriene synthase
F: Stellatatriene synthase
G: Stellatatriene synthase
H: Stellatatriene synthase
I: Stellatatriene synthase
J: Stellatatriene synthase
K: Stellatatriene synthase
L: Stellatatriene synthase
M: Stellatatriene synthase
N: Stellatatriene synthase
O: Stellatatriene synthase
P: Stellatatriene synthase
Q: Stellatatriene synthase
R: Stellatatriene synthase


Theoretical massNumber of molelcules
Total (without water)1,454,45518
Polymers1,454,45518
Non-polymers00
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
Stellatatriene synthase / SS / Stellatic acid biosynthetis gene clusters protein Stl-SS


Mass: 80803.039 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus stellatus (mold) / Gene: Stl-SS / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0P0ZEM1, Transferases; Transferring alkyl or aryl groups, other than methyl groups, stellata-2,6,19-triene synthase
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: EvSS / Type: CELL / Entity ID: all / Source: NATURAL
Source (natural)Organism: Aspergillus stellatus (mold)
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: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 108639 / Symmetry type: POINT
RefinementHighest resolution: 3.25 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00343362
ELECTRON MICROSCOPYf_angle_d0.60358662
ELECTRON MICROSCOPYf_dihedral_angle_d3.5925726
ELECTRON MICROSCOPYf_chiral_restr0.0386660
ELECTRON MICROSCOPYf_plane_restr0.0047542

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