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- EMDB-11270: E2 core of the fungal Pyruvate dehydrogenase complex with asymmet... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11270 | ||||||||||||||||||
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Title | E2 core of the fungal Pyruvate dehydrogenase complex with asymmetric interior PX30 component | ||||||||||||||||||
![]() | Fungal PDC (N. crassa). Recombinant preparation-tE2 PX30. Enforced symmetry: I2. Periphery (PX only) is absent/oversym. Core is structured. Interior is oversymm. | ||||||||||||||||||
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![]() | acetyl transferase / pyruvate dehydrogenase / protein complex / mitochondria / metabolism / tetrahedral icosahedral / TRANSFERASE | ||||||||||||||||||
Function / homology | ![]() dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / acetyl-CoA biosynthetic process from pyruvate / : Similarity search - Function | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||||||||||||||
![]() | Forsberg BO / Howard RJ / Aibara S / Mortesaei 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
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 36.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.7 KB 16.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 15.8 KB | Display | ![]() |
Images | ![]() | 64 KB | ||
Filedesc metadata | ![]() | 5.6 KB | ||
Others | ![]() ![]() | 171 MB 171 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 607.4 KB | Display | ![]() |
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Full document | ![]() | 607 KB | Display | |
Data in XML | ![]() | 20.7 KB | Display | |
Data in CIF | ![]() | 27.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zloMC ![]() 6zlmC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Fungal PDC (N. crassa). Recombinant preparation-tE2 PX30. Enforced symmetry: I2. Periphery (PX only) is absent/oversym. Core is structured. Interior is oversymm. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.12 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Half-map 1. Fungal PDC (N. crassa). Recombinant preparation-tE2...
File | emd_11270_half_map_1.map | ||||||||||||
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Annotation | Half-map 1. Fungal PDC (N. crassa). Recombinant preparation-tE2 PX30. Enforced symmetry: I2. Periphery (PX only) is absent/oversym. Core is structured. Interior is oversymm. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map 2. Fungal PDC (N. crassa). Recombinant preparation-tE2...
File | emd_11270_half_map_2.map | ||||||||||||
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Annotation | Half-map 2. Fungal PDC (N. crassa). Recombinant preparation-tE2 PX30. Enforced symmetry: I2. Periphery (PX only) is absent/oversym. Core is structured. Interior is oversymm. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Core of Pyruvate dehydrogenase complex with asymmetric interior P...
Entire | Name: Core of Pyruvate dehydrogenase complex with asymmetric interior PX component. |
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Components |
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-Supramolecule #1: Core of Pyruvate dehydrogenase complex with asymmetric interior P...
Supramolecule | Name: Core of Pyruvate dehydrogenase complex with asymmetric interior PX component. type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Dihydrolipoyllysine-residue acetyltransferase component of pyruva...
Macromolecule | Name: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO / EC number: dihydrolipoyllysine-residue acetyltransferase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 30.083316 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MRGSHHHHHH GMASMTGGQQ MGRDLYDDDD KDRWGSLVPR GSHMAAYTDV PISGMRKTIA ARLKESVTEN PHFFVSTNLS VSKLLKLRQ ALNSSADGRY KLSVNDFLIK AMGIASKRVP TVNSSWRDGV IRQFETVDVS VAVATPNGLI TPIVKGVEGK G LESISAAV ...String: MRGSHHHHHH GMASMTGGQQ MGRDLYDDDD KDRWGSLVPR GSHMAAYTDV PISGMRKTIA ARLKESVTEN PHFFVSTNLS VSKLLKLRQ ALNSSADGRY KLSVNDFLIK AMGIASKRVP TVNSSWRDGV IRQFETVDVS VAVATPNGLI TPIVKGVEGK G LESISAAV KELAKKARDG KLKPEEYQGG SISISNMGMN PAVQSFTAII NPPQAAILAV GAPQKVAVPV ENEDGTTGVS WD EQIIVTA SFDHKVVDGA VGAEWIRELK KVIENPLELL L UniProtKB: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 3 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 27.3 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-6zlo: |