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- EMDB-72639: Cryo-EM map of Mycobacterium tuberculosis pyruvate dehydrogenase ... -

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Basic information

Entry
Database: EMDB / ID: EMD-72639
TitleCryo-EM map of Mycobacterium tuberculosis pyruvate dehydrogenase complex E2p core subunit DlaT in a two-hexamer state
Map data
Sample
  • Complex: two-hexamer of dihydrolipoamide acetyltransferase of Mycobacterium tuberculosis pyruvate dehydrogenase complex
    • Protein or peptide: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
Keywordstwo-hexamer dihydrolipoamide acetyltransferase Mycobacterium tuberculosis pyruvate dehydrogenase complex / TRANSFERASE
Function / homology
Function and homology information


Cell redox homeostasis / dihydrolipoyl dehydrogenase (NADH) activity / dihydrolipoyllysine-residue succinyltransferase activity / lipoic acid binding / dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / disulfide oxidoreductase activity / pyruvate dehydrogenase complex / cellular detoxification / antioxidant activity ...Cell redox homeostasis / dihydrolipoyl dehydrogenase (NADH) activity / dihydrolipoyllysine-residue succinyltransferase activity / lipoic acid binding / dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / disulfide oxidoreductase activity / pyruvate dehydrogenase complex / cellular detoxification / antioxidant activity / tricarboxylic acid cycle / cell redox homeostasis / peptidoglycan-based cell wall / plasma membrane / cytosol
Similarity search - Function
2-oxoglutarate dehydrogenase, E2 component / : / Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) ...2-oxoglutarate dehydrogenase, E2 component / : / Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / Biotin-requiring enzyme / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Chloramphenicol acetyltransferase-like domain superfamily
Similarity search - Domain/homology
Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.51 Å
AuthorsHsu HC / Li H
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI175342 United States
CitationJournal: J Biol Chem / Year: 2026
Title: Mycobacterium tuberculosis assembles a unique hexameric E2p core of the pyruvate dehydrogenase complex.
Authors: Hao-Chi Hsu / Isabelle Bonnet / Ruslana Bryk / Huilin Li /
Abstract: The pyruvate dehydrogenase complex (PDHc) is a universally conserved multienzyme system that converts pyruvate into acetyl-CoA for entry into the TCA cycle and for NADH production. Its central ...The pyruvate dehydrogenase complex (PDHc) is a universally conserved multienzyme system that converts pyruvate into acetyl-CoA for entry into the TCA cycle and for NADH production. Its central scaffold, the dihydrolipoyl transacetylase (E2p), forms an oligomeric inner core that recruits pyruvate dehydrogenase (E1p) and dihydrolipoyl dehydrogenase (E3). All previously characterized PDHc assemblies adopt either an octahedral 24-mer or an icosahedral 60-mer E2p core, each constructed from trimeric building blocks. We recently showed that the Mycobacterium tuberculosis (Mtb) E2p protein DlaT also functions as the core of the pathogen's peroxynitrite reductase/peroxidase (PNR/P) complex. Here, using cryo-EM, we demonstrate that DlaT assembles into discrete hexamers and dodecamers at micromolar concentrations, which approximate intracellular DlaT concentrations in Mtb. Structure-guided mutagenesis combined with in vitro activity assays indicate that the hexamer represents the functional E2p core of the Mtb PDHc. This noncanonical architecture arises from unique interfaces between DlaT trimers that preclude formation of the classic spherical 24- or 60-mer structures. We propose that this specialized E2p organization enables Mtb to regulate metabolic activities and to remodel the E2p core for engagement in the PNR/P antioxidant pathway under stress. Our findings reveal an unexpected diversity in PDHc architecture and uncover a distinct organization principle for the core metabolic complex in mycobacteria.
History
DepositionSep 9, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72639.png

Downloads & links

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Map

FileDownload / File: emd_72639.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 264.96 Å		0.83 Å/pix.
x 320 pix.
= 264.96 Å		0.83 Å/pix.
x 320 pix.
= 264.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-2.872405 - 4.5071588
Average (Standard dev.)0.0032634921 (±0.11944235)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 264.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72639_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72639_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_72639_half_map_2.map
Projections & Slices
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Sample components

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Entire : two-hexamer of dihydrolipoamide acetyltransferase of Mycobacteriu...

EntireName: two-hexamer of dihydrolipoamide acetyltransferase of Mycobacterium tuberculosis pyruvate dehydrogenase complex
Components
  • Complex: two-hexamer of dihydrolipoamide acetyltransferase of Mycobacterium tuberculosis pyruvate dehydrogenase complex
    • Protein or peptide: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex

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Supramolecule #1: two-hexamer of dihydrolipoamide acetyltransferase of Mycobacteriu...

SupramoleculeName: two-hexamer of dihydrolipoamide acetyltransferase of Mycobacterium tuberculosis pyruvate dehydrogenase complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 720 KDa

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Macromolecule #1: Dihydrolipoyllysine-residue acetyltransferase component of pyruva...

MacromoleculeName: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO / EC number: dihydrolipoyllysine-residue acetyltransferase
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 25.951412 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: HLRGTTQKAS RIRQITANKT RESLQATAQL TQTHEVDMTK IVGLRARAKA AFAEREGVNL TFLPFFAKAV IDALKIHPNI NASYNEDTK EITYYDAEHL GFAVDTEQGL LSPVIHDAGD LSLAGLARAI ADIAARARSG NLKPDELSGG TFTITNIGSQ G ALFDTPIL ...String:
HLRGTTQKAS RIRQITANKT RESLQATAQL TQTHEVDMTK IVGLRARAKA AFAEREGVNL TFLPFFAKAV IDALKIHPNI NASYNEDTK EITYYDAEHL GFAVDTEQGL LSPVIHDAGD LSLAGLARAI ADIAARARSG NLKPDELSGG TFTITNIGSQ G ALFDTPIL VPPQAAMLGT GAIVKRPRVV VDASGNESIG VRSVCYLPLT YDHRLIDGAD AGRFLTTIKH RLEEGAFEAD LG L

UniProtKB: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex

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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

Concentration0.8 mg/mL
BufferpH: 7.5 / Details: 20 mM Tris, pH 7.5, 5 mM MgCl2, and 100 mM KCl
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 10 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 17053 / Average exposure time: 1.5 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4178622
CTF correctionSoftware - Name: cryoSPARC (ver. 3.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.51 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3) / Number images used: 714313
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9y72:
Structure of Mycobacterium tuberculosis pyruvate dehydrogenase complex E2p core subunit DlaT in a two-hexamer state

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