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- PDB-9s7j: Cryo-EM (200kV) structure of pyruvate decarboxylase from Neoasaia... -

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Basic information

Entry
Database: PDB / ID: 9s7j
TitleCryo-EM (200kV) structure of pyruvate decarboxylase from Neoasaia chiangmaiensis
Componentspyruvate decarboxylase
KeywordsCYTOSOLIC PROTEIN / metabolic enzyme pyruvate decarboxylase CO2 fixation
Function / homology
Function and homology information


pyruvate decarboxylase / : / pyruvate decarboxylase activity / thiamine pyrophosphate binding / magnesium ion binding / cytosol
Similarity search - Function
: / Thiamine pyrophosphate (TPP)-dependent enzyme / : / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate-binding fold / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
THIAMINE DIPHOSPHATE / pyruvate decarboxylase
Similarity search - Component
Biological speciesNeoasaia chiangmaiensis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.85 Å
Authorsvan Rooyen, J.M. / Barker, I. / Fruncillo, S. / Pandya, A. / Ozkaya, D. / Alcasabas, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)101000580European Union
CitationJournal: Adv.Synth.Catal. / Year: 2026
Title: Enantioselective Synthesis of Lactic Acid From CO2 Using a Novel Pyruvate Decarboxylase in a Scalable Biocatalytic Cascade
Authors: van Rooyen, J.M. / Barker, I. / Fruncillo, S. / Ozkaya, D. / Alcasabas, A.
History
DepositionAug 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data 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: pyruvate decarboxylase
B: pyruvate decarboxylase
C: pyruvate decarboxylase
D: pyruvate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,53512
Polymers248,7374
Non-polymers1,7988
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ALAALAARGARGAA2 - 55422 - 574
d_12MGMGMGMGAE600
d_13TPPTPPTPPTPPAF601
d_21ALAALAARGARGBB2 - 55422 - 574
d_22MGMGMGMGBG600
d_23TPPTPPTPPTPPBH601
d_31ALAALAARGARGCC2 - 55422 - 574
d_32MGMGMGMGCI600
d_33TPPTPPTPPTPPCJ601
d_41ALAALAARGARGDD2 - 55422 - 574
d_42MGMGMGMGDK600
d_43TPPTPPTPPTPPDL601

NCS oper:
IDCodeMatrixVector
1given(-0.999999983473, -0.000178051597075, 3.67667803002E-5), (-0.000178051826926, 0.999999984129, -6.24841366486E-6), (-3.67656671767E-5, -6.25495995399E-6, -0.999999999305)302.417702789, 0.0186912081901, 302.408258701
2given(-0.99999997773, -5.54552009058E-5, 0.000203626945681), (5.55802777717E-5, -0.999999809779, 0.000614290886423), (0.000203592841322, 0.000614302190385, 0.999999790591)302.368427778, 302.302162336, -0.121426747626
3given(0.999999802955, -0.000479787296375, 0.000404837992972), (-0.000479888441603, -0.999999853658, 0.000249781105775), (0.000404718091926, -0.00024997533363, -0.999999886858)-0.00449896555276, 302.439998885, 302.365222678

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Components

#1: Protein
pyruvate decarboxylase


Mass: 62184.207 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: N-terminal His-tagged / Source: (gene. exp.) Neoasaia chiangmaiensis (bacteria) / Gene: A0U93_01580 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1U9KM35, pyruvate decarboxylase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N4O7P2S / 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: PDC tetramer in complex with TPP ligands and Mg cofactors
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.059954 MDa / Experimental value: NO
Source (natural)Organism: Neoasaia chiangmaiensis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4 / Details: PBS
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 120000 X / Nominal defocus max: 2300 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.5 sec. / Electron dose: 41 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of real images: 3623

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Processing

EM software
IDNameVersionCategory
1RELION5.0.0particle selection
2EPUimage acquisition
4RELIONCTF correction
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
11RELIONclassification
12RELION3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1500000
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 314682 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 104 / Protocol: AB INITIO MODEL / Space: REAL
Atomic model buildingDetails: ModelAngelo / Source name: Other / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 44.22 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00217152
ELECTRON MICROSCOPYf_angle_d0.449923352
ELECTRON MICROSCOPYf_chiral_restr0.03912616
ELECTRON MICROSCOPYf_plane_restr0.00293060
ELECTRON MICROSCOPYf_dihedral_angle_d4.93022424
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAELECTRON MICROSCOPYNCS constraints1.07578323537E-10
ens_1d_3AAELECTRON MICROSCOPYNCS constraints3.16532726386E-13
ens_1d_4AAELECTRON MICROSCOPYNCS constraints1.89067571623E-13

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