[English] 日本語
Yorodumi
- PDB-9wyf: Crystal structure of the TC domain of a bifunctional sesterterpen... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9wyf
TitleCrystal structure of the TC domain of a bifunctional sesterterpene synthase
ComponentsAstellifadiene synthase
KeywordsBIOSYNTHETIC PROTEIN / sesterterpene synthase
Function / homology
Function and homology information


geranylfarnesyl diphosphate synthase / geranylfarnesyl diphosphate synthase activity / alcohol biosynthetic process / Lyases; Carbon-oxygen lyases; Acting on phosphates / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsLei, Z.Y. / Ma, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22377004, 82325046, 82273829, 92357305, 32571451, 32171212 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 26, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Astellifadiene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9612
Polymers41,9361
Non-polymers241
Water3,693205
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)157.353, 51.904, 56.047
Angle α, β, γ (deg.)90.000, 107.660, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

-
Components

#1: Protein Astellifadiene synthase / SS


Mass: 41936.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus stellatus (mold) / Gene: EvAS / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A169T193, Lyases; Carbon-oxygen lyases; Acting on phosphates, geranylgeranyl diphosphate synthase, geranylfarnesyl diphosphate synthase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M (NH4)2SO4, 0.1 M MES monohydrate pH 7.0, 30% (w/v) PEG monomethyl ether 5000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 27376 / % possible obs: 99.5 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 25.1
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 1387 / % possible all: 92.3

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.20.1_4487refinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→26.7 Å / SU ML: 0.2283 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.3581
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.24 1998 7.33 %
Rwork0.1923 25257 -
obs0.1958 27255 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.86 Å2
Refinement stepCycle: LAST / Resolution: 2.05→26.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2780 0 1 205 2986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722841
X-RAY DIFFRACTIONf_angle_d0.78973838
X-RAY DIFFRACTIONf_chiral_restr0.0511411
X-RAY DIFFRACTIONf_plane_restr0.0074494
X-RAY DIFFRACTIONf_dihedral_angle_d4.9142378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.090.30421400.24011664X-RAY DIFFRACTION92.09
2.09-2.150.29081490.21191787X-RAY DIFFRACTION99.33
2.15-2.210.29681380.19791788X-RAY DIFFRACTION99.79
2.21-2.290.24321510.19431812X-RAY DIFFRACTION99.75
2.29-2.370.24971430.18371825X-RAY DIFFRACTION99.8
2.37-2.460.24791380.18781818X-RAY DIFFRACTION99.69
2.46-2.570.24091410.18881800X-RAY DIFFRACTION99.79
2.57-2.710.23971490.17531796X-RAY DIFFRACTION99.64
2.71-2.880.2451370.17611826X-RAY DIFFRACTION99.85
2.88-3.10.18871360.18381831X-RAY DIFFRACTION99.8
3.1-3.410.2151550.18721810X-RAY DIFFRACTION99.54
3.41-3.90.21831390.17761827X-RAY DIFFRACTION99.44
3.9-4.910.23351460.19011826X-RAY DIFFRACTION99.25
4.91-26.70.27441360.22251847X-RAY DIFFRACTION96.4

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more