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- EMDB-47457: Variediene synthase with one cyclase (conformation 3) -

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Basic information

Entry
Database: EMDB / ID: EMD-47457
TitleVariediene synthase with one cyclase (conformation 3)
Map data
Sample
  • Complex: Variediene synthase from Emericella variecolor (EvVS) with one cyclase visible
    • Protein or peptide: Variediene synthase
  • Ligand: PYROPHOSPHATE 2-
KeywordsEnzyme / terpene / bifunctional / variediene / TRANSFERASE
Function / homology
Function and homology information


variediene synthase / (2E)-alpha-cericerene synthase / geranylfarnesyl diphosphate synthase / alcohol 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 synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
Biological speciesAspergillus stellatus (mold)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsWenger ES / Christianson DW
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)574961-0089 United States
CitationJournal: Nat Commun / Year: 2025
Title: Structure of bifunctional variediene synthase yields unique insight on biosynthetic diterpene assembly and cyclization.
Authors: Eliott S Wenger / David W Christianson /
Abstract: An unusual family of bifunctional terpene synthases has been identified in which a prenyltransferase assembles 5-carbon precursors to form C geranylgeranyl diphosphate (GGPP), which is then converted ...An unusual family of bifunctional terpene synthases has been identified in which a prenyltransferase assembles 5-carbon precursors to form C geranylgeranyl diphosphate (GGPP), which is then converted into a polycyclic product by a cyclase. Here, we report the cryo-EM structure of a massive, 495-kD bifunctional terpene synthase, variediene synthase from Emericella variecolor (EvVS). The structure reveals a hexameric prenyltransferase core sandwiched between two triads of cyclases. Surprisingly, GGPP is not channeled intramolecularly from the prenyltransferase to the cyclase, but instead is channeled intermolecularly to a non-native cyclase as indicated by substrate competition experiments. These results inform our understanding of carbon management in the greater family of bifunctional terpene synthases, hundreds of which have been identified in fungi. Using sequence similarity networks, we also report the identification of bifunctional terpene synthases in an animal, Adineta steineri, a bdelloid rotifer indigenous to freshwater environments.
History
DepositionOct 22, 2024-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47457.png

Downloads & links

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Map

FileDownload / File: emd_47457.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 384 pix.
= 414.72 Å		1.08 Å/pix.
x 384 pix.
= 414.72 Å		1.08 Å/pix.
x 384 pix.
= 414.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.0017864227 - 1.7496854
Average (Standard dev.)0.00044015047 (±0.015415105)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 414.72003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_47457_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_47457_half_map_2.map
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Variediene synthase from Emericella variecolor (EvVS) with one cy...

EntireName: Variediene synthase from Emericella variecolor (EvVS) with one cyclase visible
Components
  • Complex: Variediene synthase from Emericella variecolor (EvVS) with one cyclase visible
    • Protein or peptide: Variediene synthase
  • Ligand: PYROPHOSPHATE 2-

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Supramolecule #1: Variediene synthase from Emericella variecolor (EvVS) with one cy...

SupramoleculeName: Variediene synthase from Emericella variecolor (EvVS) with one cyclase visible
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Aspergillus stellatus (mold)

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Macromolecule #1: Variediene synthase

MacromoleculeName: Variediene synthase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: variediene synthase
Source (natural)Organism: Aspergillus stellatus (mold)
Molecular weightTheoretical: 82.57025 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MSQSSDFILN STLSSVVERS TPDIAGFCSG YELRRHHHEH LANEGSLRCR TDWEQFIGPI ERWGSCNPW EGHFGAVVLP FCKPERLAVI CYIFEYAFLY DNVVESAAKS TLNLNTDNIA LDETEYRTVR SILGTKQIQS K MLLELLSI ...String:
MGSSHHHHHH SSGLVPRGSH MSQSSDFILN STLSSVVERS TPDIAGFCSG YELRRHHHEH LANEGSLRCR TDWEQFIGPI ERWGSCNPW EGHFGAVVLP FCKPERLAVI CYIFEYAFLY DNVVESAAKS TLNLNTDNIA LDETEYRTVR SILGTKQIQS K MLLELLSI DAPRAEVVIN SWKEMISTTA KKDKTRAFNN LEEYVDYRII DTGAPFVDML MRFGMGIMLT QEEQKRIEPI VK PCYAALG LANDYFSFDI EWEEFQAESD KTTMTNAVWL FMQWENLNAE QAKRRVQEVT KQYEQQYLRN IADFAAGEGK ENI KLQTYL KAQGYQVPGN VAWSLRCPRY HPWLCKEAAS LLHQDTIQEL EAGRKPQALE EYRSRSHSES DLSDASPTFW SGSC RSSAR SSVSSAFGPP DKDISITPAI LGDEHLLGPA EYISSLPSKG VREAFIDGLN VWLVLPDHRV NQLKSIAQTL HNASL MLDD IEDHSPLRRG RPSTHMIFGT EQTINSANFL LIDVMEKVRQ LDDPRCMDIY LEEMRNLFIG QSFDLYWTRN GECPSE EQY LDMIRQKTGG LFRLLTRMMV QIAPVQQKGL ETQLASLSDV LGEFFQVRDD YKNLTEEYTG QKGFCEDLDE CKFSYPL IH ALTSQPKNVQ LRGILQQSRS AGGLDVPLKE TVLSHLRQAG SIEYTEAKMG ELMEKITDSV VSLEGETGSP NWVVRLLI H RLKV

UniProtKB: Variediene synthase

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Macromolecule #2: PYROPHOSPHATE 2-

MacromoleculeName: PYROPHOSPHATE 2- / type: ligand / ID: 2 / Number of copies: 1 / Formula: POP
Molecular weightTheoretical: 175.959 Da
Chemical component information

ChemComp-POP:
PYROPHOSPHATE 2-

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 43.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: AlphaFold Prediction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 289027
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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