[English] 日本語
Yorodumi
- PDB-9y6t: Structure of Mycobacterium tuberculosis pyruvate dehydrogenase co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9y6t
TitleStructure of Mycobacterium tuberculosis pyruvate dehydrogenase complex E2p core subunit DlaT in a hexamer state
ComponentsDihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
KeywordsTRANSFERASE / hexamer dihydrolipoamide acetyltransferase Mycobacterium tuberculosis pyruvate dehydrogenase complex
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsHsu, H.C. / Li, H.
Funding support United States, 1items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
B: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
C: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
D: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
E: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
F: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex


Theoretical massNumber of molelcules
Total (without water)155,7086
Polymers155,7086
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein
Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / Component of peroxynitrite reductase/peroxidase complex / Component of PNR/P / Dihydrolipoamide ...Component of peroxynitrite reductase/peroxidase complex / Component of PNR/P / Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex / Pyruvate dehydrogenase complex component E2 / PDH component E2


Mass: 25951.412 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: dlaT, sucB, Rv2215, MTCY190.26 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P9WIS7, dihydrolipoyllysine-residue acetyltransferase
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: hexamer of dihydrolipoamide acetyltransferase of Mycobacterium tuberculosis pyruvate dehydrogenase complex
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.36 MDa / Experimental value: NO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21
Buffer solutionpH: 7.5 / Details: 20 mM Tris, pH 7.5, 5 mM MgCl2, and 100 mM KCl
SpecimenConc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 279 K

-
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 magnification: 105000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.5 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 17053
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 5760 / Height: 4092

-
Processing

EM software
IDNameVersionCategory
1cryoSPARC3.3particle selection
2SerialEM3image acquisition
4cryoSPARC3.3CTF correction
7UCSF Chimera1.14model fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3.33D reconstruction
13PHENIX1.20.1_4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 4178622
SymmetryPoint symmetry: D3 (2x3 fold dihedral)
3D reconstructionResolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 379608 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementHighest resolution: 2.65 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00411136
ELECTRON MICROSCOPYf_angle_d0.48815102
ELECTRON MICROSCOPYf_dihedral_angle_d4.8181572
ELECTRON MICROSCOPYf_chiral_restr0.041776
ELECTRON MICROSCOPYf_plane_restr0.0051986

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more