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- EMDB-61579: Cryo-EM structure of chalcone synthase (CHS) from Physcomitrella ... -

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Basic information

Entry
Database: EMDB / ID: EMD-61579
TitleCryo-EM structure of chalcone synthase (CHS) from Physcomitrella patens in the presence of CHIL
Map data
Sample
  • Complex: Chalcone synthase (CHS) complexed with chalcone isomerase-like (CHIL) protein
    • Protein or peptide: Chalcone synthase
Keywordschalcone synthase / chalcone isomerase-like protein / catalytic promiscuity / flavonoids / protein-protein interaction / metabolon / TRANSFERASE
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)
Methodsingle 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, 1 items
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, 2024-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61579.png

Downloads & links

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Map

FileDownload / File: emd_61579.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.79 Å/pix.
x 256 pix.
= 201.728 Å		0.79 Å/pix.
x 256 pix.
= 201.728 Å		0.79 Å/pix.
x 256 pix.
= 201.728 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.788 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.31705117 - 0.49307454
Average (Standard dev.)0.0001227954 (±0.0102078)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 201.72798 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_61579_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61579_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Chalcone synthase (CHS) complexed with chalcone isomerase-like (C...

EntireName: Chalcone synthase (CHS) complexed with chalcone isomerase-like (CHIL) protein
Components
  • Complex: Chalcone synthase (CHS) complexed with chalcone isomerase-like (CHIL) protein
    • Protein or peptide: Chalcone synthase

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Supramolecule #1: Chalcone synthase (CHS) complexed with chalcone isomerase-like (C...

SupramoleculeName: Chalcone synthase (CHS) complexed with chalcone isomerase-like (CHIL) protein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Physcomitrium patens (plant)

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Macromolecule #1: Chalcone synthase

MacromoleculeName: Chalcone synthase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: chalcone synthase
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 42.615027 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MASAGDVTRA ALPRAQPRAE GPACVLGIGT AVPPAEFLQS EYPDFFFNIT NCGEKEALKA KFKRICDKSG IRKRHMFLTE EVLKANPGI CTYMEPSLNV RHDIVVVQVP KLAAEAAQKA IKEWGGRKSD ITHIVFATTS GVNMPGADHA LAKLLGLKPT V KRVMMYQT ...String:
MASAGDVTRA ALPRAQPRAE GPACVLGIGT AVPPAEFLQS EYPDFFFNIT NCGEKEALKA KFKRICDKSG IRKRHMFLTE EVLKANPGI CTYMEPSLNV RHDIVVVQVP KLAAEAAQKA IKEWGGRKSD ITHIVFATTS GVNMPGADHA LAKLLGLKPT V KRVMMYQT GCFGGASVLR VAKDLAENNK GARVLAVASE VTAVTYRAPS ENHLDGLVGS ALFGDGAGVY VVGSDPKPEV EK PLFEVHW AGETILPESD GAIDGHLTEA GLIFHLMKDV PGLISKNIEK FLNEARKPVG SPAWNEMFWA VHPGGPAILD QVE AKLKLT KDKMQGSRDI LSEFGNMSSA SVLFVLDQIR HRSVKMGAST LGEGSEFGFF IGFGPGLTLE VLVLRAAPNS A

UniProtKB: Chalcone synthase

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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

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6dx7

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1277322
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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