2024-05-01 REL PDBe PDBe PDBe 2021-01-07 2021-02-10 2021-02-10 2024-05-01 Cryo-EM map of Icosahedrally averaged native core of Pyruvate Dehydrogenase Complex from Ch. thermophilum Skalidis I Kyrilis FL Tueting C Semchonok DA Kastritis PL Dihydrolipoyl, transacetylase, E2, Pyruvate, TRANSFERASE Kyrilis FL Semchonok DA Skalidis I Tuting C Hamdi F O'Reilly FJ Rappsilber J Kastritis PL Integrative structure of a 10-megadalton eukaryotic pyruvate dehydrogenase complex from native cell extracts. Cell Rep US 34 108727 108727 2021 33567276 doi:10.1016/j.celrep.2021.108727 2211-1247 7bgj FULLOVERLAP Native 60-mer core of Pyruvate Dehydrogenase Complex Native 60-mer core of Pyruvate Dehydrogenase Complex 0 1 Chaetomium thermophilum var. thermophilum DSM 1495 3 Acetyltransferase component of pyruvate dehydrogenase complex Chaetomium thermophilum var. thermophilum DSM 1495 0.048777487999999994 1 LEVO MLAQVLRRQALQHVRLARAAAPSLTRWYASYPPHTIVKMPALSPTMTSGNIGAWQKKPGDAITPGEVLVEIETDKAQMDF EFQEEGVLAKILKETGEKDVAVGSPIAVLVEEGTDINAFQNFTLEDAGGDAAAPAAPAKEELAKAETAPTPASTSAPEPE ETTSTGKLEPALDREPNVSFAAKKLAHELDVPLKALKGTGPGGKITEEDVKKAASAPAAAAAAPGAAYQDIPISNMRKTI ATRLKESVSENPHFFVTSELSVSKLLKLRQALNSSAEGRYKLSVNDFLIKAIAVACKRVPAVNSSWRDGVIRQFDTVDVS VAVATPTGLITPIVKGVEAKGLETISATVKELAKKARDGKLKPEDYQGGTISISNMGMNPAVERFTAIINPPQAAILAVG TTKKVAVPVENEDGTTGVEWDDQIVVTASFDHKVVDGAVGAEWMRELKKVVENPLELLL G0S4X6 2.3.1.12 singleParticle particle 0.3 7.4 200.0 NH4CH2COOH Ammonium acetate ETHANE 95 277 FEI VITROBOT MARK IV
For plunging, blot force 2 and blotting time of 6 sec were applied..
TFS GLACIOS OTHER BRIGHT FIELD FIELD EMISSION GUN 200 100.0 2.7 0.8 2.0 45000.0 44067.0 OTHER NITROGEN 77.15 103.15 14.7 FEI FALCON III (4k x 4k) INTEGRATING 2593 30.0 1 205251
Automated selection with template derived from manual selection
 6CT0 1 I SIMULTANEOUS ITERATIVE (SIRT) 6.9 FSC 0.143 CUT-OFF RELION 3.0 29516 ANGULAR RECONSTITUTION RELION 3.0 ANGULAR RECONSTITUTION RELION 3.0 5 RELION 3.0 emd_12181.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 250 250 250 0 0 0 250 250 250 794.125 794.125 794.125 90.0 90.0 90.0 X Y Z -0.057240035 0.12619737 0.00019970845 0.0066095362 3.1765 3.1765 3.1765 0.026 AUTHOR Symmetrically averaged (Icosahedral Symmetry) Pyruvate Dehydrogenase Complex core from Ch. thermophilum. 6CT0 A 444-647 PDB experimental model FLEXIBLE FIT
The initial model was used to generate our model using MODELLER. This inital model was fitted into the density using ChimeraX and refined in real space using PHENIX.
REAL 103.25 emd_12181_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 250 250 250 0 0 0 250 250 250 794.125 794.125 794.125 90.0 90.0 90.0 X Y Z -0.0776511 0.15971187 0.0003576083 0.007593935 3.1765 3.1765 3.1765 AUTHOR Asymmetrical Pyruvate Dehydrogenase Complex from Ch. thermophilum. emd_12181_additional_6.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 250 250 250 0 0 0 250 250 250 794.125 794.125 794.125 90.0 90.0 90.0 X Y Z -0.07893464 0.13347286 0.00016201468 0.007030972 3.1765 3.1765 3.1765 AUTHOR Asymmetrical Pyruvate Dehydrogenase Complex core from Ch. thermophilum. emd_12181_additional_5.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 250 250 250 0 0 0 250 250 250 794.125 794.125 794.125 90.0 90.0 90.0 X Y Z -0.08481563 0.15096806 0.00016554966 0.007890747 3.1765 3.1765 3.1765 AUTHOR Asymmetrical Pyruvate Dehydrogenase Complex core from Ch. thermophilum. Half-map 2 emd_12181_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 250 250 250 0 0 0 250 250 250 794.125 794.125 794.125 90.0 90.0 90.0 X Y Z -0.085485145 0.14648043 0.00021822835 0.00788898 3.1765 3.1765 3.1765 AUTHOR Asymmetrical Pyruvate Dehydrogenase Complex core from Ch. thermophilum. Half-map 1 emd_12181_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 250 250 250 0 0 0 250 250 250 794.125 794.125 794.125 90.0 90.0 90.0 X Y Z -0.08935737 0.16393793 0.0003314399 0.008518473 3.1765 3.1765 3.1765 AUTHOR Asymmetrical Pyruvate Dehydrogenase Complex from Ch. thermophilum, Half-map 2. emd_12181_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 250 250 250 0 0 0 250 250 250 794.125 794.125 794.125 90.0 90.0 90.0 X Y Z -0.09155813 0.16975676 0.00034126063 0.008475565 3.1765 3.1765 3.1765 AUTHOR Asymmetrical Pyruvate Dehydrogenase Complex from Ch. thermophilum, Half-map 1. emd_12181_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 250 250 250 0 0 0 250 250 250 794.125 794.125 794.125 90.0 90.0 90.0 X Y Z -0.059539177 0.12918563 0.0002127369 0.0066120834 3.1765 3.1765 3.1765 AUTHOR Symmetrically averaged (Icosahedral Symmetry) Pyruvate Dehydrogenase Complex core from Ch. thermophilum, Half-map 2. emd_12181_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 250 250 250 0 0 0 250 250 250 794.125 794.125 794.125 90.0 90.0 90.0 X Y Z -0.05626628 0.12887979 0.00020992891 0.0066500176 3.1765 3.1765 3.1765 AUTHOR Symmetrically averaged (Icosahedral Symmetry) Pyruvate Dehydrogenase Complex core from Ch. thermophilum, Half-map 1.