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- PDB-6zlm: Dihydrolipoyllysine-residue acetyltransferase component of fungal... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zlm | ||||||||||||||||||
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Title | Dihydrolipoyllysine-residue acetyltransferase component of fungal pyruvate dehydrogenase complex with protein X bound | ||||||||||||||||||
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![]() | TRANSFERASE / acetyl transferase / pyruvate dehydrogenase / protein complex / mitochondria / metabolism / tetrahedral icosahedral | ||||||||||||||||||
Function / homology | ![]() dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / acetyl-CoA biosynthetic process from pyruvate / : Similarity search - Function | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å | ||||||||||||||||||
![]() | Forsberg, B.O. / Aibara, S. / Howard, R.J. / Mortezaei, N. / Lindahl, E. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Arrangement and symmetry of the fungal E3BP-containing core of the pyruvate dehydrogenase complex. Authors: B O Forsberg / S Aibara / R J Howard / N Mortezaei / E Lindahl / ![]() ![]() Abstract: The pyruvate dehydrogenase complex (PDC) is a multienzyme complex central to aerobic respiration, connecting glycolysis to mitochondrial oxidation of pyruvate. Similar to the E3-binding protein (E3BP) ...The pyruvate dehydrogenase complex (PDC) is a multienzyme complex central to aerobic respiration, connecting glycolysis to mitochondrial oxidation of pyruvate. Similar to the E3-binding protein (E3BP) of mammalian PDC, PX selectively recruits E3 to the fungal PDC, but its divergent sequence suggests a distinct structural mechanism. Here, we report reconstructions of PDC from the filamentous fungus Neurospora crassa by cryo-electron microscopy, where we find protein X (PX) interior to the PDC core as opposed to substituting E2 core subunits as in mammals. Steric occlusion limits PX binding, resulting in predominantly tetrahedral symmetry, explaining previous observations in Saccharomyces cerevisiae. The PX-binding site is conserved in (and specific to) fungi, and complements possible C-terminal binding motifs in PX that are absent in mammalian E3BP. Consideration of multiple symmetries thus reveals a differential structural basis for E3BP-like function in fungal PDC. | ||||||||||||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 4.4 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 311.5 KB | Display | |
Data in CIF | ![]() | 477.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 11268MC ![]() 6zloC C: citing same article ( M: map data used to model this data |
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Similar structure data | |
EM raw data | ![]() Data size: 305.5 Data #1: Aligned and dose-weighted micrographs of native N. crassa Pyruvate dehydrogenase [micrographs - single frame]) |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 48677.395 Da / Num. of mol.: 60 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: P20285, dihydrolipoyllysine-residue acetyltransferase #2: Protein/peptide | Mass: 1124.378 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Details: Uniprot Q7RWS2 Source: (natural) ![]() |
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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 |
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Sample preparation
Component | Name: endogenous pyruvate dehydrogenase complex form Neurospora crassa Type: COMPLEX Details: Catalytic (C-terminal) domain of Dihydrolipoyllysine-residue acetyltransferase (E2-component of pyruvate dehydrogenase complex) Entity ID: all / Source: NATURAL |
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Molecular weight | Value: 7 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() Organelle: mitochondria |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 35 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON II (4k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: T (tetrahedral) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21129 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||
Refinement | Stereochemistry target values: CDL v1.2 | ||||||||||||||||||||||||||||
Refine LS restraints |
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