[English] 日本語
Yorodumi
- EMDB-62579: Cryo-EM structure of C-Methyltransferase from Rhododendron dauricum -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-62579
TitleCryo-EM structure of C-Methyltransferase from Rhododendron dauricum
Map data
Sample
  • Complex: C-Methyltransferase from Rhododendron dauricum
    • Protein or peptide: C-Methyltransferase from Rhododendron dauricum
KeywordsMethyltransferase / Dimer / TRANSFERASE
Biological speciesRhododendron dauricum (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsYe YM / Dai ZD / Zhang MZ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J Am Chem Soc / Year: 2025
Title: Molecular and Structural Characterization of a Chalcone di--Methyltransferase RdCMT from and Its Application in De Novo Biosynthesis of Farrerol in .
Authors: Meng Zhang / Yang-Oujie Bao / Zonglin Dai / Zhilan Qian / Haishuang Yu / Jia-Jing Zhou / Yi Chen / Zilong Wang / Kaituo Wang / Menghao Cai / Min Ye /
Abstract: Methylation plays a crucial role in drug design and optimization. While numerous methyltransferases have been characterized from plants, -methyltransferases, particularly those targeting phenolic ...Methylation plays a crucial role in drug design and optimization. While numerous methyltransferases have been characterized from plants, -methyltransferases, particularly those targeting phenolic skeletons, are rare. In this study, we identified a novel di--methyltransferase RdCMT from the medicinal plant . RdCMT catalyzes a sequential two-step 3'-/5'--methylation of naringenin chalcone, leading to the biosynthesis of farrerol. RdCMT exhibited a strict substrate specificity for chalcones. Through combinatorial catalysis, a series of -methylated flavonoids were synthesized. Moreover, farrerol was synthesized de novo in and with yields of 0.4 mg/g (dry weight) and 149.0 mg/L, respectively. The structure of RdCMT was determined using cryo-electron microscopy (cryo-EM), revealing that residues R328 and G296 significantly influence the substrate specificity of RdCMT. This work not only introduces a potent biocatalyst for the preparation of -methylated flavonoids but also offers insights into the catalytic mechanisms of -methyltransferases.
History
DepositionDec 4, 2024-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_62579.png

Downloads & links

-
Map

FileDownload / File: emd_62579.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.4877802 - 0.71780914
Average (Standard dev.)0.0003085626 (±0.01669806)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 217.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_62579_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_62579_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : C-Methyltransferase from Rhododendron dauricum

EntireName: C-Methyltransferase from Rhododendron dauricum
Components
  • Complex: C-Methyltransferase from Rhododendron dauricum
    • Protein or peptide: C-Methyltransferase from Rhododendron dauricum

-
Supramolecule #1: C-Methyltransferase from Rhododendron dauricum

SupramoleculeName: C-Methyltransferase from Rhododendron dauricum / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rhododendron dauricum (plant)

-
Macromolecule #1: C-Methyltransferase from Rhododendron dauricum

MacromoleculeName: C-Methyltransferase from Rhododendron dauricum / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhododendron dauricum (plant)
Molecular weightTheoretical: 43.111586 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MDQEKELPTS NKIDVENGDG SNRAEEEELC SYSNAIELAF SVVLPMVMKA AVELQVLDII AKAGPRAQLS PSQIASQLPA AALRCSPDA PKMLDRMLCL LASHSILTCS AVDFHSDDHN DSPSTAAAAL EDKRLYGLTP LAKYFVPNQD GVSLGPLMCL V QDKVCMKS ...String:
MDQEKELPTS NKIDVENGDG SNRAEEEELC SYSNAIELAF SVVLPMVMKA AVELQVLDII AKAGPRAQLS PSQIASQLPA AALRCSPDA PKMLDRMLCL LASHSILTCS AVDFHSDDHN DSPSTAAAAL EDKRLYGLTP LAKYFVPNQD GVSLGPLMCL V QDKVCMKS WYELKGAVLE GGVPFMRVYG VESFDYPGTD PRFNEVLNNA MVNYSTIFLK KLMQSSYNGF EQVETLVDVG GG LGVALEL ITSKYPHIKA INFDLPHVIK HAKPYPGLEH VGGDMFESVP KGDAIFMKGV LHDWSDDLCL KLLKNCYKAL PDN GKIIAV ERILPEMPNS AGKGIFLMDL QMMTHHLGGR ERTQQEYFDL AISAGFSGIR LECLVCNLWV IELYK

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration10 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number grids imaged: 1 / 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 / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 60207
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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