2024-07-24 REL PDBe PDBe PDBe 2023-03-23 2023-05-31 2023-05-31 2024-07-24 Not funded Cryo-EM reconstruction of the native 24-mer E2o core of the 2-oxoglutarate dehydrogenase complex of C. thermophilum at 3.35 A resolution Skalidis I Tueting C Kyrilis FL Hamdi F Kastritis PL Dihydrolipoyl Succinyltransferase, E2, Oxoglutarate, a-Ketoglutarate, TRANSFERASE Skalidis I Kyrilis FL Tuting C Hamdi F Trager TK Belapure J Hause G Fratini M O'Reilly FJ Heilmann I Rappsilber J Kastritis PL Structural analysis of an endogenous 4-megadalton succinyl-CoA-generating metabolon. Commun Biol UK 6 552 552 2023 37217784 doi:10.1038/s42003-023-04885-0 2399-3642 8oiu FULLOVERLAP Native 24-mer core of Oxoglutarate Dehydrogenase Complex Native 24-mer core of Oxoglutarate Dehydrogenase Complex 0 1 Thermochaetoides thermophila DSM 1495 3 Dihydrolipoyllysine-residue succinyltransferase Thermochaetoides thermophila DSM 1495 0.045987004 1 LEVO MLYRGLRMAARAAPKFAVLNTHAALRQLPLQFQHVRTYADKIIKVPQMAESITEGTLKQWNKAVGDYVEADEEIATIETD KIDVAVNAPEAGVIKEFFVNEEDTVLVGQDLVRLEVGGEKPAEAAKEQPKAAAPEPKVEEKKVPEAPAPEPSKTAAPAPA PPKQEAPASPKPASKPAETPAVTLGNREERRVKMNRMRLRIAERLKQSQNTAASLTTFNEVDMSALIEFRNKYKDEVLKK TGVKLGFMSAFSRAVVLAIRDLPVVNASIEGPNGGDTIVYRDYVDISVAVATEKGLVTPVVRNAETMDLITIEKTIAELG KKARDGKLTIEDMAGGTFTISNGGVFGSLMGTPIINLPQSAVLGLHAIKERPVAVNGKVEIRPMMYLALTYDHRLLDGRE AVQFLVKVKEYIEDPRKMLL G0SAX9 2.3.1.61 singleParticle particle 0.3 7.4 200.0 NH4CH2COOH Ammonium acetate Quantifoil R2/1 COPPER 300 CARBON HOLEY GLOW DISCHARGE ETHANE 95 277 FEI VITROBOT MARK IV
For plunging, blot force 0 and blotting time of 4 sec were applied..
TFS GLACIOS OTHER BRIGHT FIELD FIELD EMISSION GUN 200 100.0 2.7 0.8 2.0 92000.0 OTHER NITROGEN 77.15 103.15 FEI FALCON III (4k x 4k) INTEGRATING 21381 30.0 1 1300
Template picking was directly applied
 EMD-13844 50 O SIMULTANEOUS ITERATIVE (SIRT) 3.35 FSC 0.143 CUT-OFF cryoSPARC 3.1 Local refinement (NEW)
Particles were symmetry expanded for the final reconstruction, then local reconstruction was performed without symmetry application.
69028 RANDOM ASSIGNMENT cryoSPARC 3.1 Ab-initio reconstruction MAXIMUM LIKELIHOOD cryoSPARC 3.1 Local refinement (NEW) 200 2133.0 cryoSPARC 3.1 2D classification emd_16900.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 208 208 208 0 0 0 208 208 208 326.10242 326.10242 326.10242 90.0 90.0 90.0 X Y Z -2.3572903 5.9476595 -0.003834117 0.22103816 1.5678 1.5678 1.5678 0.8 AUTHOR Cryo-EM reconstruction of the native 24-mer E2o core of the 2-oxoglutarate dehydrogenase complex of C. thermophilum. 7Q5Q all PDB experimental model FLEXIBLE FIT
Initial fitting was performed in ChimeraX v1.2, then real-space refined in PHENIX v1.19
REAL emd_16900_msk_1.map emd_16900_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 0 0 0 192 192 192 301.0176 301.0176 301.0176 90.0 90.0 90.0 X Y Z -1.8166873 4.473056 0.011294818 0.120323025 1.5678 1.5678 1.5678 AUTHOR Cryo-EM reconstruction of the native asymmetric complex of the 2-oxoglutarate dehydrogenase complex of C. thermophilum. emd_16900_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 208 208 208 0 0 0 208 208 208 326.10242 326.10242 326.10242 90.0 90.0 90.0 X Y Z -0.5715986 1.8554239 0.0036370396 0.14512926 1.5678 1.5678 1.5678 AUTHOR Cryo-EM reconstruction of the native 24-mer E2o core of the 2-oxoglutarate dehydrogenase complex of C. thermophilum, Half-Map B. emd_16900_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 208 208 208 0 0 0 208 208 208 326.10242 326.10242 326.10242 90.0 90.0 90.0 X Y Z -0.5806802 1.8488096 0.0034458893 0.14518969 1.5678 1.5678 1.5678 AUTHOR Cryo-EM reconstruction of the native 24-mer E2o core of the 2-oxoglutarate dehydrogenase complex of C. thermophilum, Half-Map A.