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Yorodumi- PDB-7uom: Endogenous dihydrolipoamide acetyltransferase (E2) core of pyruva... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7uom | ||||||||||||
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Title | Endogenous dihydrolipoamide acetyltransferase (E2) core of pyruvate dehydrogenase complex from bovine kidney | ||||||||||||
Components | Acetyltransferase component of pyruvate dehydrogenase complex | ||||||||||||
Keywords | TRANSFERASE / e2 / 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 / identical protein binding Similarity search - Function | ||||||||||||
Biological species | Bos taurus (cattle) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||
Authors | Liu, S. / Xia, X. / Zhen, J. / Li, Z.H. / Zhou, Z.H. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7uom.cif.gz | 2.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7uom.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7uom.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7uom_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7uom_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7uom_validation.xml.gz | 306.2 KB | Display | |
Data in CIF | 7uom_validation.cif.gz | 464.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uo/7uom ftp://data.pdbj.org/pub/pdb/validation_reports/uo/7uom | HTTPS FTP |
-Related structure data
Related structure data | 26650MC 7uolC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 69142.594 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: kidney / Tissue: kidney References: UniProt: F1N690, dihydrolipoyllysine-residue acetyltransferase |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Endogenous dihydrolipoamide acetyltransferase (E2) core of pyruvate dehydrogenase complex from bovine kidney Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Molecular weight | Value: 0.069 MDa / Experimental value: NO |
Source (natural) | Organism: Bos taurus (cattle) / Cellular location: mitochondrial matrix / Organ: kidney / Organelle: mitochondria / Tissue: kidney |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: PELCO Ultrathin Carbon with Lacey Carbon |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 1800 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 8 sec. / Electron dose: 45 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Movie frames/image: 40 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 33138 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: BACKBONE TRACE / Space: REAL | ||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6CT0 Accession code: 6CT0 / Source name: PDB / Type: experimental model |