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- EMDB-66379: Cryo-EM structure of PbSS -

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Basic information

Entry
Database: EMDB / ID: EMD-66379
TitleCryo-EM structure of PbSS
Map data
Sample
  • Cell: Sesterbrasiliatriene synthase PbSS
    • Protein or peptide: Sesterbrasiliatriene synthase PbSS
KeywordsSesterbrasiliatriene synthase PbSS / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


geranylfarnesyl diphosphate synthase / Lyases; Carbon-oxygen lyases; Acting on phosphates / alcohol biosynthetic process / ketone biosynthetic process / mycotoxin biosynthetic process / geranylgeranyl diphosphate synthase / 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
Sesterbrasiliatriene synthase PbSS
Similarity search - Component
Biological speciesPenicillium brasilianum (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsBai L / Lyu RQ
Funding support China, 1 items
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, 2025-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateFeb 11, 2026-
Current statusFeb 11, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66379.png

Downloads & links

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Map

FileDownload / File: emd_66379.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 400 pix.
= 296. Å		0.74 Å/pix.
x 400 pix.
= 296. Å		0.74 Å/pix.
x 400 pix.
= 296. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.72641987 - 1.0452801
Average (Standard dev.)0.000042317984 (±0.021721786)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 296.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_66379_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_66379_half_map_2.map
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Sample components

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Entire : Sesterbrasiliatriene synthase PbSS

EntireName: Sesterbrasiliatriene synthase PbSS
Components
  • Cell: Sesterbrasiliatriene synthase PbSS
    • Protein or peptide: Sesterbrasiliatriene synthase PbSS

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Supramolecule #1: Sesterbrasiliatriene synthase PbSS

SupramoleculeName: Sesterbrasiliatriene synthase PbSS / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Penicillium brasilianum (fungus)

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Macromolecule #1: Sesterbrasiliatriene synthase PbSS

MacromoleculeName: Sesterbrasiliatriene synthase PbSS / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
EC number: Lyases; Carbon-oxygen lyases; Acting on phosphates
Source (natural)Organism: Penicillium brasilianum (fungus)
Molecular weightTheoretical: 83.286156 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDFLSGAFHY SDSVNPSKYS PRPSDYFGTL PFRTSRFERE AADVTADYLR KWQKAVKADN PERKDLVFHG STTTLGHFVS WAYPECIPD RVDLCTQICD FGFYWDDVTD SVNVQENAEI TQDLALALLS ELTLGQRLEP KLEINKIVVQ MLWGVLDKDR K SGLEMIKF ...String:
MDFLSGAFHY SDSVNPSKYS PRPSDYFGTL PFRTSRFERE AADVTADYLR KWQKAVKADN PERKDLVFHG STTTLGHFVS WAYPECIPD RVDLCTQICD FGFYWDDVTD SVNVQENAEI TQDLALALLS ELTLGQRLEP KLEINKIVVQ MLWGVLDKDR K SGLEMIKF WKGHLDGQAE SAHNNMSFEE YTKHRLSEVG ARWAVEVGCW SLGINLSREK KDSVAHFVNK GLLAAALMND YY SFNKEFD EHQRAGSMDR LQNGLGILMR EYGYTETEAR SILREEIRKG ERAIMDGYIA WRESADSSSE SHELNRYIVM IIL MIGGIT FWSSHASRYH RDDLITTAGD RAMIVGKFQC SMRLLDGYPP PNRWKSATSS NDISGRKRKS WSDSNGVDTH GACY TNGSS NRAKRNGTEA GHKANGHDSM DIYTAPFLKA PSEVCEAPYE YINSLQGKNM RNKFMDALNH WLCVPAPSMQ IIKNI VQML HNSSLMLDDI EDESPLRRGQ PVAHTFYGIS QTINSANFVY VKSVKETSRL KNPICMEIFT DELSNLHTGQ SLDLYW RYH GRCPSINEYI MMVDNKTGGL FRLMLRLMEA ESPAASSASL VKLLTLTGRY YQIRDDYLNL TSVEYTSKKG FCEDLDE GK FSLPLLHLLN HTRHPDRITA PLFNRASGAR SLAREVKVHI IQAMDEAGTF EYAQGVLKYL HEEIMRTLDE VEADLGRN T EARILLLGLG L

UniProtKB: Sesterbrasiliatriene synthase PbSS

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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

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 476438
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION

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