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- EMDB-26650: Endogenous dihydrolipoamide acetyltransferase (E2) core of pyruva... -

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Basic information

Entry
Database: EMDB / ID: EMD-26650
TitleEndogenous dihydrolipoamide acetyltransferase (E2) core of pyruvate dehydrogenase complex from bovine kidney
Map data
Sample
  • Complex: Endogenous dihydrolipoamide acetyltransferase (E2) core of pyruvate dehydrogenase complex from bovine kidney
    • Protein or peptide: Acetyltransferase component of pyruvate dehydrogenase complex
Function / homology
Function and homology information


Signaling by Retinoic Acid / Pyruvate metabolism / Regulation of pyruvate dehydrogenase (PDH) complex / Glyoxylate metabolism and glycine degradation / pyruvate dehydrogenase (NAD+) activity / dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / mitochondrial pyruvate dehydrogenase complex / identical protein binding
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-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. ...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-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / 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 speciesBos taurus (cattle) / cattle (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLiu S / Xia X / Zhen J / Li ZH / Zhou ZH
Funding support United States, 3 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DMR-1548924 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071940 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI060567 United States
CitationJournal: Cell Discov / Year: 2022
Title: Structures and comparison of endogenous 2-oxoglutarate and pyruvate dehydrogenase complexes from bovine kidney.
Authors: Shiheng Liu / Xian Xia / James Zhen / Zihang Li / Z Hong Zhou /
Abstract: The α-keto acid dehydrogenase complex family catalyzes the essential oxidative decarboxylation of α-keto acids to yield acyl-CoA and NADH. Despite performing the same overarching reaction, members ...The α-keto acid dehydrogenase complex family catalyzes the essential oxidative decarboxylation of α-keto acids to yield acyl-CoA and NADH. Despite performing the same overarching reaction, members of the family have different component structures and structural organization between each other and across phylogenetic species. While native structures of α-keto acid dehydrogenase complexes from bacteria and fungi became available recently, the atomic structure and organization of their mammalian counterparts in native states remain unknown. Here, we report the cryo-electron microscopy structures of the endogenous cubic 2-oxoglutarate dehydrogenase complex (OGDC) and icosahedral pyruvate dehydrogenase complex (PDC) cores from bovine kidney determined at resolutions of 3.5 Å and 3.8 Å, respectively. The structures of multiple proteins were reconstructed from a single lysate sample, allowing direct structural comparison without the concerns of differences arising from sample preparation and structure determination. Although native and recombinant E2 core scaffold structures are similar, the native structures are decorated with their peripheral E1 and E3 subunits. Asymmetric sub-particle reconstructions support heterogeneity in the arrangements of these peripheral subunits. In addition, despite sharing a similar monomeric fold, OGDC and PDC E2 cores have distinct interdomain and intertrimer interactions, which suggests a means of modulating self-assembly to mitigate heterologous binding between mismatched E2 species. The lipoyl moiety lies near a mobile gatekeeper within the interdomain active site of OGDC E2 and PDC E2. Analysis of the twofold related intertrimer interface identified secondary structural differences and chemical interactions between icosahedral and cubic geometries of the core. Taken together, our study provides a direct structural comparison of OGDC and PDC from the same source and offers new insights into determinants of interdomain interactions and of architecture diversity among α-keto acid dehydrogenase complexes.
History
DepositionApr 13, 2022-
Header (metadata) releaseNov 30, 2022-
Map releaseNov 30, 2022-
UpdateNov 30, 2022-
Current statusNov 30, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_26650.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 576 pix.
= 783.36 Å
1.36 Å/pix.
x 576 pix.
= 783.36 Å
1.36 Å/pix.
x 576 pix.
= 783.36 Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.017067049 - 0.050618216
Average (Standard dev.)-1.929863e-05 (±0.0013542303)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 783.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_26650_msk_1.map
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Half map: #1

Fileemd_26650_half_map_1.map
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Half map: #2

Fileemd_26650_half_map_2.map
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Sample components

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Entire : Endogenous dihydrolipoamide acetyltransferase (E2) core of pyruva...

EntireName: Endogenous dihydrolipoamide acetyltransferase (E2) core of pyruvate dehydrogenase complex from bovine kidney
Components
  • Complex: Endogenous dihydrolipoamide acetyltransferase (E2) core of pyruvate dehydrogenase complex from bovine kidney
    • Protein or peptide: Acetyltransferase component of pyruvate dehydrogenase complex

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Supramolecule #1: Endogenous dihydrolipoamide acetyltransferase (E2) core of pyruva...

SupramoleculeName: Endogenous dihydrolipoamide acetyltransferase (E2) core of pyruvate dehydrogenase complex from bovine kidney
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bos taurus (cattle) / Organ: kidney / Tissue: kidney / Organelle: mitochondria / Location in cell: mitochondrial matrix
Molecular weightTheoretical: 69 KDa

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Macromolecule #1: Acetyltransferase component of pyruvate dehydrogenase complex

MacromoleculeName: Acetyltransferase component of pyruvate dehydrogenase complex
type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO / EC number: dihydrolipoyllysine-residue acetyltransferase
Source (natural)Organism: cattle (cattle) / Organ: kidney / Tissue: kidney
Molecular weightTheoretical: 69.142594 KDa
SequenceString: MWRVCARRAQ NAAPRAGFGA RWTAFREEPG APCVTPQAGS ALARCSSKTP GYGRVRALCG WSPVSRATPR NRVLLQLWGS PSRRWYSLP PHQKVPLPSL SPTMQAGTIA RWEKKEGEKI NEGELIAEVE TDKATVGFES VEECYMAKIL VAEGTRDVPV G AIICITVD ...String:
MWRVCARRAQ NAAPRAGFGA RWTAFREEPG APCVTPQAGS ALARCSSKTP GYGRVRALCG WSPVSRATPR NRVLLQLWGS PSRRWYSLP PHQKVPLPSL SPTMQAGTIA RWEKKEGEKI NEGELIAEVE TDKATVGFES VEECYMAKIL VAEGTRDVPV G AIICITVD KPEDVEAFKN YTLDSSAAPA PPAAPAPTPA APAPSPTPSA QAPGSSYPTH MQVLLPALSP TMTMGTVQRW EK KVGEKLN EGDLLAEIET DKATIGFEVQ EEGYLAKILI PEGTRDVPLG TPLCIIVEKE ADIPAFADYR PAEVTDLKPP APP PIPSPA APVPPAPQPV APPPSAPRPA APAGPKGRVF VSPLAKKLAA EKGIDLTQVK GTGPDGRIIK KDIDSFVPTK AAPT PAAAV PPPSPGVAPV PTGVFTDIPI SNIRRVIAQR LMQSKQTIPH YYLSIDVNMG EVLLVRKELN KMLEGKSKIS VNDFI IKAS ALACLKVPEA NSSWMDTVIR QNHVVDISVA VSTPAGLITP IVFNAHIKGL ETIANDVVSL ATKAREGKLQ PHEFQG GTF TISNLGMFGI KNFSAIINPP QACILAIGAS EDRLVPADNE KGFDVASMMS VTLSCDHRVV DGAVGAQWLA EFRKYLE KP ITMLL

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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

BufferpH: 7
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 8.0 sec. / Average electron dose: 45.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 33138
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:
SoftwareName: UCSF ChimeraX
RefinementSpace: REAL / Protocol: BACKBONE TRACE
Output model

PDB-7uom:
Endogenous dihydrolipoamide acetyltransferase (E2) core of pyruvate dehydrogenase complex from bovine kidney

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