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- EMDB-54642: Cryo-EM (200kV) structure of pyruvate decarboxylase from Neoasaia... -

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Basic information

Entry
Database: EMDB / ID: EMD-54642
TitleCryo-EM (200kV) structure of pyruvate decarboxylase from Neoasaia chiangmaiensis
Map datab-factor-sharpened masked map
Sample
  • Complex: PDC tetramer in complex with TPP ligands and Mg cofactors
    • Protein or peptide: pyruvate decarboxylase
  • Ligand: MAGNESIUM ION
  • Ligand: THIAMINE DIPHOSPHATE
Keywordsmetabolic enzyme pyruvate decarboxylase CO2 fixation / CYTOSOLIC PROTEIN
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
pyruvate decarboxylase
Similarity search - Component
Biological speciesNeoasaia chiangmaiensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
Authorsvan Rooyen JM / Barker I / Fruncillo S / Pandya A / Ozkaya D / Alcasabas A
Funding supportEuropean Union, 1 items
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 JM / Barker I / Fruncillo S / Ozkaya D / Alcasabas A
History
DepositionAug 4, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54642.png

Downloads & links

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Map

FileDownload / File: emd_54642.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationb-factor-sharpened masked map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 360 pix.
= 302.4 Å		0.84 Å/pix.
x 360 pix.
= 302.4 Å		0.84 Å/pix.
x 360 pix.
= 302.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.022
Minimum - Maximum-0.051708847 - 0.099465996
Average (Standard dev.)0.00007702443 (±0.0024229335)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 302.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54642_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map 1

Fileemd_54642_half_map_1.map
Annotationhalf-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map 2

Fileemd_54642_half_map_2.map
Annotationhalf-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PDC tetramer in complex with TPP ligands and Mg cofactors

EntireName: PDC tetramer in complex with TPP ligands and Mg cofactors
Components
  • Complex: PDC tetramer in complex with TPP ligands and Mg cofactors
    • Protein or peptide: pyruvate decarboxylase
  • Ligand: MAGNESIUM ION
  • Ligand: THIAMINE DIPHOSPHATE

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Supramolecule #1: PDC tetramer in complex with TPP ligands and Mg cofactors

SupramoleculeName: PDC tetramer in complex with TPP ligands and Mg cofactors
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Neoasaia chiangmaiensis (bacteria)
Molecular weightTheoretical: 59.954 KDa

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Macromolecule #1: pyruvate decarboxylase

MacromoleculeName: pyruvate decarboxylase / type: protein_or_peptide / ID: 1 / Details: N-terminal His-tagged / Number of copies: 4 / Enantiomer: LEVO / EC number: pyruvate decarboxylase
Source (natural)Organism: Neoasaia chiangmaiensis (bacteria)
Molecular weightTheoretical: 62.184207 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MAYTVGMYLA ERLAQIGLKH HFAVAGDYNL VLLDQLLLNK DMEQIYCCNE LNCGFSAEGY ARAQGAAAA VVTFSVGAIS AMNAIGGAYA ENLPVILISG APNSNDHGSG HVLHHTIGTT DYGYQLEMVR HLTCAAESIV S AENAPAKI ...String:
MGSSHHHHHH SSGLVPRGSH MAYTVGMYLA ERLAQIGLKH HFAVAGDYNL VLLDQLLLNK DMEQIYCCNE LNCGFSAEGY ARAQGAAAA VVTFSVGAIS AMNAIGGAYA ENLPVILISG APNSNDHGSG HVLHHTIGTT DYGYQLEMVR HLTCAAESIV S AENAPAKI DHVIRTALRE RKPAYLEIAC NVAGAECVRP GPVSSLLPET PSDLTSLQAA LDASLAWLAP RDRVVLLVGS KL RAADAQA VSVELADRMG CAVTIMAAAK GFFPEDHPCY RGLYWGEVSS PGVQELVESA DGIICLAPVF NDYSTVGWNA WPK GDNVLL AEPDRVTVAG RSYEGIALRD FIKGMTARAL SKPVTAQGTT APRLELAQAK GDAPLTNDEM TRQIQALLNR DTTL TAETG DSWFNATRMN LPGGARVELE MQWGHIGWSV PSAFGNAMGS QDRRHVLMVG DGSFQLTAQE VAQMIRYELP VIIFL VNNR GYVIEIAIHD GPYNYIKNWD YAGLIAAFNA GEGHGLGLHA KTGDELQDAI EKAVANKRGP TLIECSIARD DCTSEL VNW GKRVAATNSR RPAAD

UniProtKB: pyruvate decarboxylase

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: THIAMINE DIPHOSPHATE

MacromoleculeName: THIAMINE DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: TPP
Molecular weightTheoretical: 425.314 Da
Chemical component information

ChemComp-TPP:
THIAMINE DIPHOSPHATE

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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

Concentration2 mg/mL
BufferpH: 7.4 / Details: PBS
GridModel: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number real images: 3623 / Average exposure time: 3.5 sec. / Average electron dose: 41.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 120000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 1500000
CTF correctionSoftware - Name: RELION / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: SGD
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D2 (2x2 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 314682
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 4 / Avg.num./class: 315000 / Software - Name: RELION

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: ModelAngelo
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 104
Output model

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

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