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Yorodumi- EMDB-11271: E2 core of the fungal Pyruvate dehydrogenase complex with asymmet... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11271 | ||||||||||||||||||
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Title | E2 core of the fungal Pyruvate dehydrogenase complex with asymmetric interior PX261 component | ||||||||||||||||||
Map data | Fungal PDC (N. crassa). Recombinant preparation-tE2/PX261. Enforced symmetry: I2. Periphery (PX only) is absent. Core is structured. Interior is oversymm. | ||||||||||||||||||
Sample |
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Biological species | Neurospora crassa (fungus) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||||||||
Authors | Forsberg BO / Lindahl E / Aibara S / Howard RJ / Mortezaei N | ||||||||||||||||||
Funding support | Sweden, European Union, 5 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11271.map.gz | 44 MB | EMDB map data format | |
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Header (meta data) | emd-11271-v30.xml emd-11271.xml | 12.7 KB 12.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11271_fsc.xml | 13.6 KB | Display | FSC data file |
Images | emd_11271.png | 86.4 KB | ||
Others | emd_11271_additional.map.gz emd_11271_additional_1.map.gz | 202.4 MB 202.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11271 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11271 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_11271.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Fungal PDC (N. crassa). Recombinant preparation-tE2/PX261. Enforced symmetry: I2. Periphery (PX only) is absent. Core is structured. Interior is oversymm. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Fungal PDC (N. crassa). Recombinant preparation-tE2/PX261. Enforced symmetry:...
File | emd_11271_additional.map | ||||||||||||
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Annotation | Fungal PDC (N. crassa). Recombinant preparation-tE2/PX261. Enforced symmetry: I2. Periphery (PX only) is absent. Core is structured. Interior is oversymm. Unmasked | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Fungal PDC (N. crassa). Recombinant preparation-tE2/PX261. Enforced symmetry:...
File | emd_11271_additional_1.map | ||||||||||||
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Annotation | Fungal PDC (N. crassa). Recombinant preparation-tE2/PX261. Enforced symmetry: I2. Periphery (PX only) is absent. Core is structured. Interior is oversymm. Unmasked | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : E2 core of the fungal Pyruvate dehydrogenase complex with asymmet...
Entire | Name: E2 core of the fungal Pyruvate dehydrogenase complex with asymmetric inetrior PX261 component |
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Components |
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-Supramolecule #1: E2 core of the fungal Pyruvate dehydrogenase complex with asymmet...
Supramolecule | Name: E2 core of the fungal Pyruvate dehydrogenase complex with asymmetric inetrior PX261 component type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Neurospora crassa (fungus) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 31.4 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |