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- PDB-9j1w: Endogenous dihydrolipoamide acetyltransferase (E2) core of pyruva... -

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Basic information

Entry
Database: PDB / ID: 9j1w
TitleEndogenous dihydrolipoamide acetyltransferase (E2) core of pyruvate dehydrogenase complex from pig heart
ComponentsAcetyltransferase component of pyruvate dehydrogenase complex
KeywordsTRANSFERASE / pyruvate dehydrogenase complex / dihydrolipoamide acetyltransferase / endogenous / STRUCTURAL PROTEIN
Function / homology
Function and homology information


dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / pyruvate decarboxylation to acetyl-CoA / pyruvate dehydrogenase complex / mitochondrial matrix
Similarity search - Function
Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / Dihydrolipoamide acetyltransferase/Pyruvate dehydrogenase protein X 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) ...Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / Dihydrolipoamide acetyltransferase/Pyruvate dehydrogenase protein X 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
Acetyltransferase component of pyruvate dehydrogenase complex
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsWang, C. / Zhang, X. / Chang, Y.J.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2018YFA0507700 China
National Natural Science Foundation of China (NSFC)32200980 China
CitationJournal: Nat Commun / Year: 2025
Title: Dynamics of the mammalian pyruvate dehydrogenase complex revealed by in-situ structural analysis.
Authors: Chen Wang / Cheng Ma / Yuanyou Xu / Shenghai Chang / Hangjun Wu / Chunlan Yan / Jinghua Chen / Yongping Wu / Shaoya An / Jiaqi Xu / Qin Han / Yujie Jiang / Zhinong Jiang / Xiakun Chu / ...Authors: Chen Wang / Cheng Ma / Yuanyou Xu / Shenghai Chang / Hangjun Wu / Chunlan Yan / Jinghua Chen / Yongping Wu / Shaoya An / Jiaqi Xu / Qin Han / Yujie Jiang / Zhinong Jiang / Xiakun Chu / Haichun Gao / Xing Zhang / Yunjie Chang /
Abstract: The multi-enzyme pyruvate dehydrogenase complex (PDHc) links glycolysis to the citric acid cycle and plays vital roles in metabolism, energy production, and cellular signaling. Although all ...The multi-enzyme pyruvate dehydrogenase complex (PDHc) links glycolysis to the citric acid cycle and plays vital roles in metabolism, energy production, and cellular signaling. Although all components have been individually characterized, the intact PDHc structure remains unclear, hampering our understanding of its composition and dynamical catalytic mechanisms. Here, we report the in-situ architecture of intact mammalian PDHc by cryo-electron tomography. The organization of peripheral E1 and E3 components varies substantially among the observed PDHcs, with an average of 21 E1 surrounding each PDHc core, and up to 12 E3 locating primarily along the pentagonal openings. In addition, we observed dynamic interactions of the substrate translocating lipoyl domains (LDs) with both E1 and E2, and the interaction interfaces were further analyzed by molecular dynamics simulations. By revealing intrinsic dynamics of PDHc peripheral compositions, our findings indicate a distinctive activity regulation mechanism, through which the number of E1, E3 and functional LDs may be coordinated to meet constantly changing demands of metabolism.
History
DepositionAug 5, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetyltransferase component of pyruvate dehydrogenase complex
AA: Acetyltransferase component of pyruvate dehydrogenase complex
AB: Acetyltransferase component of pyruvate dehydrogenase complex
B: Acetyltransferase component of pyruvate dehydrogenase complex
BA: Acetyltransferase component of pyruvate dehydrogenase complex
BB: Acetyltransferase component of pyruvate dehydrogenase complex
C: Acetyltransferase component of pyruvate dehydrogenase complex
CA: Acetyltransferase component of pyruvate dehydrogenase complex
CB: Acetyltransferase component of pyruvate dehydrogenase complex
D: Acetyltransferase component of pyruvate dehydrogenase complex
DA: Acetyltransferase component of pyruvate dehydrogenase complex
DB: Acetyltransferase component of pyruvate dehydrogenase complex
E: Acetyltransferase component of pyruvate dehydrogenase complex
EA: Acetyltransferase component of pyruvate dehydrogenase complex
EB: Acetyltransferase component of pyruvate dehydrogenase complex
F: Acetyltransferase component of pyruvate dehydrogenase complex
FA: Acetyltransferase component of pyruvate dehydrogenase complex
FB: Acetyltransferase component of pyruvate dehydrogenase complex
G: Acetyltransferase component of pyruvate dehydrogenase complex
GA: Acetyltransferase component of pyruvate dehydrogenase complex
GB: Acetyltransferase component of pyruvate dehydrogenase complex
H: Acetyltransferase component of pyruvate dehydrogenase complex
HA: Acetyltransferase component of pyruvate dehydrogenase complex
HB: Acetyltransferase component of pyruvate dehydrogenase complex
I: Acetyltransferase component of pyruvate dehydrogenase complex
IA: Acetyltransferase component of pyruvate dehydrogenase complex
J: Acetyltransferase component of pyruvate dehydrogenase complex
JA: Acetyltransferase component of pyruvate dehydrogenase complex
K: Acetyltransferase component of pyruvate dehydrogenase complex
KA: Acetyltransferase component of pyruvate dehydrogenase complex
L: Acetyltransferase component of pyruvate dehydrogenase complex
LA: Acetyltransferase component of pyruvate dehydrogenase complex
M: Acetyltransferase component of pyruvate dehydrogenase complex
MA: Acetyltransferase component of pyruvate dehydrogenase complex
N: Acetyltransferase component of pyruvate dehydrogenase complex
NA: Acetyltransferase component of pyruvate dehydrogenase complex
O: Acetyltransferase component of pyruvate dehydrogenase complex
OA: Acetyltransferase component of pyruvate dehydrogenase complex
P: Acetyltransferase component of pyruvate dehydrogenase complex
PA: Acetyltransferase component of pyruvate dehydrogenase complex
Q: Acetyltransferase component of pyruvate dehydrogenase complex
QA: Acetyltransferase component of pyruvate dehydrogenase complex
R: Acetyltransferase component of pyruvate dehydrogenase complex
RA: Acetyltransferase component of pyruvate dehydrogenase complex
S: Acetyltransferase component of pyruvate dehydrogenase complex
SA: Acetyltransferase component of pyruvate dehydrogenase complex
T: Acetyltransferase component of pyruvate dehydrogenase complex
TA: Acetyltransferase component of pyruvate dehydrogenase complex
UA: Acetyltransferase component of pyruvate dehydrogenase complex
V: Acetyltransferase component of pyruvate dehydrogenase complex
VA: Acetyltransferase component of pyruvate dehydrogenase complex
W: Acetyltransferase component of pyruvate dehydrogenase complex
WA: Acetyltransferase component of pyruvate dehydrogenase complex
X: Acetyltransferase component of pyruvate dehydrogenase complex
XA: Acetyltransferase component of pyruvate dehydrogenase complex
Y: Acetyltransferase component of pyruvate dehydrogenase complex
YA: Acetyltransferase component of pyruvate dehydrogenase complex
Z: Acetyltransferase component of pyruvate dehydrogenase complex
ZA: Acetyltransferase component of pyruvate dehydrogenase complex
a: Acetyltransferase component of pyruvate dehydrogenase complex


Theoretical massNumber of molelcules
Total (without water)4,155,51060
Polymers4,155,51060
Non-polymers00
Water00
1


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

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Components

#1: Protein ...
Acetyltransferase component of pyruvate dehydrogenase complex


Mass: 69258.492 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: A0A5G2QLQ1, dihydrolipoyllysine-residue acetyltransferase
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: dihydrolipoamide acetyltransferase (E2) core / Type: TISSUE / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Sus scrofa (pig)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN 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: 1300 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 52 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 68914 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 378 / Num. of volumes extracted: 120840
RefinementCross valid method: NONE

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