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- EMDB-72224: Cryo-EM structure of a Paracoccus Trimethylamine N-oxide Demethyl... -

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Basic information

Entry
Database: EMDB / ID: EMD-72224
TitleCryo-EM structure of a Paracoccus Trimethylamine N-oxide Demethylase mutant (D220A/D367A)in Complex with TMAO
Map data
Sample
  • Complex: Structure of trimethylamine N-oxide demethylase
    • Protein or peptide: Trimethylamine N-oxide Demethylase
  • Ligand: ZINC ION
  • Ligand: trimethylamine oxide
KeywordsTrimethylamine N-Oxide demethylase / paracoccus / substrate channeling / cryo-EM / METAL BINDING PROTEIN
Biological speciesParacoccus sp. DMF (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsThach T / Subramanian R
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Elife / Year: 2026
Title: Bifunctional Architecture Enables Substrate Catalysis and Channeling in Paracoccus TMAO Demethylase
Authors: Thach T / Dhanabalan K / Maurya S / Han-Hallet Y / Quan S / Allison J / Ramanathan G / Subramanian R
History
DepositionAug 20, 2025-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72224.png

Downloads & links

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Map

FileDownload / File: emd_72224.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 352 pix.
= 289.344 Å		0.82 Å/pix.
x 352 pix.
= 289.344 Å		0.82 Å/pix.
x 352 pix.
= 289.344 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.2213851 - 1.6867577
Average (Standard dev.)0.0010332346 (±0.0492827)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 289.344 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_72224_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_72224_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 : Structure of trimethylamine N-oxide demethylase

EntireName: Structure of trimethylamine N-oxide demethylase
Components
  • Complex: Structure of trimethylamine N-oxide demethylase
    • Protein or peptide: Trimethylamine N-oxide Demethylase
  • Ligand: ZINC ION
  • Ligand: trimethylamine oxide

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Supramolecule #1: Structure of trimethylamine N-oxide demethylase

SupramoleculeName: Structure of trimethylamine N-oxide demethylase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Paracoccus sp. DMF (bacteria)
Molecular weightTheoretical: 252 KDa

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Macromolecule #1: Trimethylamine N-oxide Demethylase

MacromoleculeName: Trimethylamine N-oxide Demethylase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus sp. DMF (bacteria)
Molecular weightTheoretical: 86.915094 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSAITYPGLL RPGPPRPSGL RVASPVSRAP AQERHTVTGG GALLLPLAQG DRVTVINAEG GQRAELVAVD MQGRPGLLGP ASDEPHGLR RALSSGEDSL TRLARGIAAR GIDLSKNHAI TLFGAESPAG DRAEFTAEGA GWLIACAPGD PMDPESGDTA S PLTLLIDR ...String:
MSAITYPGLL RPGPPRPSGL RVASPVSRAP AQERHTVTGG GALLLPLAQG DRVTVINAEG GQRAELVAVD MQGRPGLLGP ASDEPHGLR RALSSGEDSL TRLARGIAAR GIDLSKNHAI TLFGAESPAG DRAEFTAEGA GWLIACAPGD PMDPESGDTA S PLTLLIDR ASPRAKQGFD LPDPLADPIL DIRVKSATAE AYLVRAGEYI QIQDVDGRQC TAFQCFDARK LDRGIQNPLD VT TTRTILG HSYAMPGLHA KYFDQDNTPL VEVVQDTCGR HDAFAMACSS KYYDDIGYPG HANCSDNFNG ALAEYGVDPR KGW MAANFF FNTWIDAHGV LMTDEPWSRP GDYVLLRALT DVVCVSSACP ADTSPANGWH LSDIHVRSYA ASERFQRAVA WRPM PESEP IMTRQTAFHD NFAALTRDFI EYKGFWLPNT FPNSSPEEEY RSCRNGVAMM DLSALRKFEV TGPDSEALMQ WVLTR DVKK LGVGQVVYSA MCYPHGGMVD DGTLFRMGPD RFRWIGGTDY GGEWMREQAQ ALGLNVMIRA STDQLHNLAV QGPKSR AVM NAAFWTAPHQ TAIPELGWFR WTVGRVNGPN GAPVVVSRTG YTGELGYEIF CHPKDGAEVF AAVAEAGAPH GIKPMGL AA LDLLRIEAGL IFADYEFTDQ TDPFEAGIGF TVPLKTKPDD FIGREALIRR KENPRWKLVG IEIDSRIPAH HGDCLHIG R AQIGEITSAM WSPLLDKQIA LARVDVTHAD EGTEIEVGKL DGQQKRLPAR ITAFPHYDPK KERPRSHHHH HH

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #3: trimethylamine oxide

MacromoleculeName: trimethylamine oxide / type: ligand / ID: 3 / Number of copies: 2 / Formula: TMO
Molecular weightTheoretical: 75.11 Da
Chemical component information

ChemComp-TMO:
trimethylamine oxide

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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

Concentration1.0 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMTris-HClTris(hydroxymethyl)aminomethane hydrochloride
150.0 mMNaClSodium Chloride

Details: 20 mM Tris-HCl, 150 mM NaCl
GridModel: UltrAuFoil R1.2/1.3 / Support film - Material: GOLD / Support film - topology: CONTINUOUS / Support film - Film thickness: 11
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: vitrification.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number grids imaged: 1 / Number real images: 60 / Average exposure time: 1.8 sec. / Average electron dose: 56.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.1 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 200982
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: ab initio construction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 143707
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 50
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Chain ID: A / Chain - Residue range: 1-924 / Chain - Source name: AlphaFold / Chain - Initial model type: in silico model / Details: The initial model consisted of monomer
SoftwareName: PHENIX (ver. 1.12.1)
Detailsreal refinement was done using Phenix
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9q5a:
Cryo-EM structure of a Paracoccus Trimethylamine N-oxide Demethylase mutant (D220A/D367A)in Complex with TMAO

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