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- PDB-9q5l: Cryo-EM structure of a Paracoccus Trimethylamine N-oxide Demethyl... -

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Basic information

Entry
Database: PDB / ID: 9q5l
TitleCryo-EM structure of a Paracoccus Trimethylamine N-oxide Demethylase in complex with DMA, HCHO
Componentstrimethylamine N-oxide demethylase
KeywordsMETAL BINDING PROTEIN / Trimethylamine N-Oxide demethylase / paracoccus / substrate channeling / cryo-EM
Function / homologyDIMETHYLAMINE / FORMYL GROUP
Function and homology information
Biological speciesParacoccus sp. DMF (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsThach, T. / Subramanian, R.
Funding support1items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: trimethylamine N-oxide demethylase
B: trimethylamine N-oxide demethylase
C: trimethylamine N-oxide demethylase
D: trimethylamine N-oxide demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)348,29410
Polymers348,0124
Non-polymers2816
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
trimethylamine N-oxide demethylase


Mass: 87003.117 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus sp. DMF (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FOR / FORMYL GROUP


Mass: 30.026 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMN / DIMETHYLAMINE


Mass: 45.084 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H7N / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: Structure of trimethylamine N-oxide demethylase / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.252 MDa / Experimental value: YES
Source (natural)Organism: Paracoccus sp. DMF (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5 / Details: 20 mM Tris-HCl, 150 mM NaCl
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris(hydroxymethyl)aminomethane hydrochlorideTris-HCl1
2150 mMSodium ChlorideNaCl1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: vitrification

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 700 nm / Cs: 0.1 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 1.8 sec. / Electron dose: 56.8 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 60
EM imaging opticsEnergyfilter name: GIF Bioquantum

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.4.1particle selection
7PHENIX1.12.1model fitting
9PHENIX1.21.1model refinement
13cryoSPARC4.4.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 200982
3D reconstructionResolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 190338 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL / Details: real refinement was done using Phenix
Atomic model buildingChain residue range: 1-924 / Details: The initial model consisted of monomer / Source name: AlphaFold / Type: in silico model

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