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- PDB-9jl6: Cryo-EM structure of chalcone synthase (CHS) from Physcomitrella ... -

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Basic information

Entry
Database: PDB / ID: 9jl6
TitleCryo-EM structure of chalcone synthase (CHS) from Physcomitrella patens in the presence of CHIL
ComponentsChalcone synthase
KeywordsTRANSFERASE / chalcone synthase / chalcone isomerase-like protein / catalytic promiscuity / flavonoids / protein-protein interaction / metabolon
Function / homology
Function and homology information


chalcone synthase / naringenin-chalcone synthase activity / polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
Chalcone/stilbene synthase, active site / Chalcone and stilbene synthases active site. / Chalcone/stilbene synthase, N-terminal / Chalcone and stilbene synthases, N-terminal domain / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Thiolase-like
Similarity search - Domain/homology
Biological speciesPhyscomitrium patens (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.18 Å
AuthorsSato, K. / Yokoyama, T. / Tanaka, Y. / Imaizumi, R. / Yasuda, A. / Yanai, T. / Yamashita, S. / Waki, T. / Tsunashima, M. / Nakayama, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: Cryo-EM structure of chalcone synthase (CHS) from Physcomitrella patens in the presence of CHIL
Authors: Sato, K. / Yokoyama, T. / Tanaka, Y. / Imaizumi, R. / Yasuda, A. / Yanai, T. / Yamashita, S. / Waki, T. / Tsunashima, M. / Nakayama, T.
History
DepositionSep 18, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data 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: Chalcone synthase
B: Chalcone synthase


Theoretical massNumber of molelcules
Total (without water)85,2302
Polymers85,2302
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 Chalcone synthase


Mass: 42615.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physcomitrium patens (plant) / Gene: PHYPA_029015 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q2VAZ3, chalcone 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: Chalcone synthase (CHS) complexed with chalcone isomerase-like (CHIL) protein
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Physcomitrium patens (plant)
Source (recombinant)Organism: Escherichia coli BL21 (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1277322 / Symmetry type: POINT

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