2023-08-23 REL PDBe PDBe PDBe 2023-05-24 2023-08-16 2023-08-16 2023-08-23 Agence Nationale de la Recherche (ANR) ANR-13-JSV8-0003 France Agence Nationale de la Recherche (ANR) ANR-18-CE92-0003 France Single particle cryo-EM structure of homohexameric 2-oxoglutarate dehydrogenase OdhA from Corynebacterium glutamicum following reaction with the 2-oxoglutarate analogue succinyl phosphonate Yang L Mechaly AM Bellinzoni M 2-oxoglutarate dehydrogenase; ODH, OXIDOREDUCTASE Yang L Wagner T Mechaly A Boyko A Bruch EM Megrian D Gubellini F Alzari PM Bellinzoni M High resolution cryo-EM and crystallographic snapshots of the actinobacterial two-in-one 2-oxoglutarate dehydrogenase. Nat Commun UK 14 4851 4851 2023 37563123 doi:10.1038/s41467-023-40253-6 2041-1723 Yang L Wagner T Mechaly A Boyko A Bruch EM Megrian D Gubellini F Alzari PM Bellinzoni M High resolution cryo-EM and crystallographic snapshots of the large actinobacterial 2-oxoglutarate dehydrogenase: an all-in-one fusion with unique properties Biorxiv US 2023 doi:10.1101/2023.02.23.529587 2692-8205 8p5w FULLOVERLAP Homohexameric 2-oxoglutarate dehydrogenase Homohexameric 2-oxoglutarate dehydrogenase 0 1 Corynebacterium glutamicum ATCC 13032 0.808 2-oxoglutarate dehydrogenase E1/E2 component Corynebacterium glutamicum ATCC 13032 0.134972078 6 Escherichia coli BL21(DE3) LEVO GSMSSASTFGQNAWLVDEMFQQFQKDPKSVDKEWRELFEAQGGPNTTPATTEAQPSAPKESAKPAPKAAPAAKAAPRVET KPADKTAPKAKESSVPQQPKLPEPGQTPIRGIFKSIAKNMDISLEIPTATSVRDMPARLMFENRAMVNDQLKRTRGGKIS FTHIIGYAMVKAVMAHPDMNNSYDVIDGKPTLIVPEHINLGLAIDLPQKDGSRALVVAAIKETEKMNFSEFLAAYEDIVA RSRKGKLTMDDYQGVTVSLTNPGGIGTRHSVPRLTKGQGTIIGVGSMDYPAEFQGASEDRLAELGVGKLVTITSTYDHRV IQGAVSGEFLRTMSRLLTDDSFWDEIFDAMNVPYTPMRWAQDVPNTGVDKNTRVMQLIEAYRSRGHLIADTNPLSWVQPG MPVPDHRDLDIETHNLTIWDLDRTFNVGGFGGKETMTLREVLSRLRAAYTLKVGSEYTHILDRDERTWLQDRLEAGMPKP TQAEQKYILQKLNAAEAFENFLQTKYVGQKRFSLEGAEALIPLMDSAIDTAAGQGLDEVVIGMPHRGRLNVLFNIVGKPL ASIFNEFEGQMEQGQIGGSGDVKYHLGSEGQHLQMFGDGEIKVSLTANPSHLEAVNPVMEGIVRAKQDYLDKGVDGKTVV PLLLHGDAAFAGLGIVPETINLAKLRGYDVGGTIHIVVNNQIGFTTTPDSSRSMHYATDYAKAFGCPVFHVNGDDPEAVV WVGQLATEYRRRFGKDVFIDLVCYRLRGHNEADDPSMTQPKMYELITGRETVRAQYTEDLLGRGDLSNEDAEAVVRDFHD QMESVFNEVKEGGKKQAEAQTGITGSQKLPHGLETNISREELLELGQAFANTPEGFNYHPRVAPVAKKRVSSVTEGGIDW AWGELLAFGSLANSGRLVRLAGEDSRRGTFTQRHAVAIDPATAEEFNPLHELAQSKGNNGKFLVYNSALTEYAGMGFEYG YSVGNEDSIVAWEAQFGDFANGAQTIIDEYVSSGEAKWGQTSKLILLLPHGYEGQGPDHSSARIERFLQLCAEGSMTVAQ PSTPANHFHLLRRHALSDLKRPLVIFTPKSMLRNKAAASAPEDFTEVTKFQSVINDPNVADAAKVKKVMLVSGKLYYELA KRKEKDGRDDIAIVRIEMLHPIPFNRISEALAGYPNAEEVLFVQDEPANQGPWPFYQEHLPELIPNMPKMRRVSRRAQSS TATGVAKVHQLEEKQLIDEAFEA Q8NRC3 1.2.4.2 MAGNESIUM ION 2.4305e-05 6 MG ACETYL COENZYME *A 0.000809571 6 ACO (4~{S})-4-[(2~{R})-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-2~{H}-1,3-thiazol-2-yl]-4-oxidanyl-4-phosphono-butanoic acid 0.0006083909999999999 6 QSP singleParticle particle 12.0 7.5 20.0 HEPES-Na 500.0 NaCl EMS Lacey Carbon COPPER 200 PLASMA CLEANING OTHER ETHANE 100 277 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.8 2.2 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 BIOQUANTUM (6k x 4k) 1 16647 1.4 40.0
Each image was composed by 60 frames
 1 Ab initio model from cryoSPARC D3 2.26 FSC 0.143 CUT-OFF cryoSPARC 646352 MAXIMUM LIKELIHOOD cryoSPARC MAXIMUM LIKELIHOOD cryoSPARC cryoSPARC emd_17455.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 448 448 448 0 0 0 448 448 448 385.28 385.28 385.28 90.0 90.0 90.0 Z Y X -1.748818 66.571915000000004 0.012396597 1.183449 0.86 0.86 0.86 1.0 AUTHOR OdhA_SP main_map_dens_mod 8P5T PDB experimental model FLEXIBLE FIT REAL emd_17455_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 448 448 448 0 0 0 448 448 448 385.28 385.28 385.28 90.0 90.0 90.0 X Y Z -0.3316206 1.2276161 0.0018420651 0.043143455 0.86 0.86 0.86 AUTHOR OdhA_SP half_map_1_no_mask_cryoSPARC emd_17455_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 448 448 448 0 0 0 448 448 448 385.28 385.28 385.28 90.0 90.0 90.0 X Y Z -0.3084086 1.235654 0.0018335495 0.04314491 0.86 0.86 0.86 AUTHOR OdhA_SP half_map_2_no_mask_cryoSPARC