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Yorodumi- PDB-6zlm: Dihydrolipoyllysine-residue acetyltransferase component of fungal... -
+Open data
-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 | ||||||||||||||||||
Components |
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Keywords | TRANSFERASE / acetyl transferase / pyruvate dehydrogenase / protein complex / mitochondria / metabolism / tetrahedral icosahedral | ||||||||||||||||||
Function / homology | Function and homology information dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / acetyl-CoA biosynthetic process from pyruvate / : / glycolytic process Similarity search - Function | ||||||||||||||||||
Biological species | Neurospora crassa (fungus) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å | ||||||||||||||||||
Authors | Forsberg, B.O. / Aibara, S. / Howard, R.J. / Mortezaei, N. / Lindahl, E. | ||||||||||||||||||
Funding support | Sweden, European Union, 5items
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Citation | Journal: Nat Commun / Year: 2020 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
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6zlm.cif.gz | 4.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6zlm.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6zlm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/6zlm ftp://data.pdbj.org/pub/pdb/validation_reports/zl/6zlm | HTTPS FTP |
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-Related structure data
Related structure data | 11268MC 6zloC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | |
EM raw data | EMPIAR-10489 (Title: Native Pyruvate Dehydrogenase Complex from Neurospora crassa Data size: 305.5 Data #1: Aligned and dose-weighted micrographs of native N. crassa Pyruvate dehydrogenase [micrographs - single frame]) |
-Links
-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) Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (fungus) 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) Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (fungus) |
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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 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: Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (fungus) 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 |
-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: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 35 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON II (4k x 4k) |
-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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