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- PDB-9wyv: Cryo-EM structure of EvAS -

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Basic information

Entry
Database: PDB / ID: 9wyv
TitleCryo-EM structure of EvAS
ComponentsAstellifadiene synthase
KeywordsBIOSYNTHETIC PROTEIN / Astellifadiene synthase
Function / homology
Function and homology information


geranylfarnesyl diphosphate synthase activity / geranylfarnesyl diphosphate synthase / Lyases; Carbon-oxygen lyases; Acting on phosphates / alcohol biosynthetic process / mycotoxin biosynthetic process / geranylgeranyl diphosphate synthase / geranylgeranyl diphosphate synthase 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
Astellifadiene synthase
Similarity search - Component
Biological speciesAspergillus stellatus (mold)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLyu, R.Q. / Bai, L.
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 28, 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

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Assembly

Deposited unit
A: Astellifadiene synthase
B: Astellifadiene synthase
C: Astellifadiene synthase
D: Astellifadiene synthase
E: Astellifadiene synthase
F: Astellifadiene synthase


Theoretical massNumber of molelcules
Total (without water)492,9626
Polymers492,9626
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
Astellifadiene synthase / SS


Mass: 82160.289 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus stellatus (mold) / Gene: EvAS / Production host: Escherichia coli (E. coli)
References: UniProt: A0A169T193, Lyases; Carbon-oxygen lyases; Acting on phosphates, geranylgeranyl diphosphate synthase, geranylfarnesyl diphosphate 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: EvAS / 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
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23064 / Symmetry type: POINT

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