2025-05-07 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _em_admin.last_update PDBe PDBe 2023-04-14 2024-10-30 2024-10-30 2025-05-07 Swiss National Science Foundation 31003A_182567 Switzerland Cryo-EM structure of human tRNA ligase RTCB in complex with human PYROXD1. Loeff L Kroupova A Asanovic I Boneberg F Pfleiderer MM Ferdigg A Ackle F Martinez J Jinek M tRNA ligase, PYROXD1, RTCB, Flavoprotein, Ligase Loeff L Kroupova A Asanovic I Boneberg FM Pfleiderer MM Riermeier L Leitner A Ferdigg A Ackle F Martinez J Jinek M Mechanistic basis for PYROXD1-mediated protection of the human tRNA ligase complex against oxidative inactivation. Nat.Struct.Mol.Biol. US 2025 40069351 doi:10.1038/s41594-025-01516-6 1545-9985 Loeff L Kroupova A Asanovic I Boneberg F Pfleiderer MM Ferdigg A Ackle F Martinez J Jinek M Mechanistic basis for oxidative stress protection of the human tRNA ligase complex by the oxidoreductase PYROXD1 BioRxiv US 2023 doi:10.1101/2023.04.06.535761 2692-8205 8orj FULLOVERLAP Cryo-EM structure of human RTCB in complex with human PYROXD1. Cryo-EM structure of human RTCB in complex with human PYROXD1. 0 1 2
In vitro reconstituted protein complex
Homo sapiens RNA-splicing ligase RtcB homolog Homo sapiens 0.055556444999999996 1 Spodoptera frugiperda LEVO SNAMSRSYNDELQFLEKINKNCWRIKKGFVPNMQVEGVFYVNDALEKLMFEELRNACRGGGVGGFLPAMKQIGNVAALPG IVHRSIGLPDVHSGYGFAIGNMAAFDMNDPEAVVSPGGVGFDINCGVRLLRTNLDESDVQPVKEQLAQAMFDHIPVGVGS KGVIPMNAKDLEEALEMGVDWSLREGYAWAEDKEHCEEYGRMLQADPNKVSARAKKRGLPQLGTLGAGNHYAEIQVVDEI FNEYAAKKMGIDHKGQVCVMIHSGSRGLGHQVATDALVAMEKAMKRDKIIVNDRQLACARIASPEGQDYLKGMAAAGNYA WVNRSSMTFLTRQAFAKVFNTTPDDLDLHVIYDVSHNIAKVEQHVVDGKERTLLVHRKGSTRAFPPHHPLIAVDYQLTGQ PVLIGGTMGTCSYVLTGTEQGMTETFGTTCHGAGRALSRAKSRRNLDFQDVLDKLADMGIAIRVASPKLVMEEAPESYKN VTDVVNTCHDAGISKKAIKLRPIAVIKG Q9Y3I0 6.5.1.8 Pyridine nucleotide-disulfide oxidoreductase domain-containing protein 1 Homo sapiens 0.056016858999999995 1 Escherichia coli LEVO GPMEAARPPPTAGKFVVVGGGIAGVTCAEQLATHFPSEDILLVTASPVIKAVTNFKQISKILEEFDVEEQSSTMLGKRFP NIKVIESGVKQLKSEEHCIVTEDGNQHVYKKLCLCAGAKPKLICEGNPYVLGIRDTDSAQEFQKQLTKAKRIMIIGNGGI ALELVYEIEGCEVIWAIKDKAIGNTFFDAGAAEFLTSKLIAEKSEAKIAHKRTRYTTEGRKKEARSKSKADNVGSALGPD WHEGLNLKGTKEFSHKIHLETMCEVKKIYLQDEFRILKKKSFTFPRDHKSVTADTEMWPVYVELTNEKIYGCDFIVSATG VTPNVEPFLHGNSFDLGEDGGLKVDDHMHTSLPDIYAAGDICTTSWQLSPVWQQMRLWTQARQMGWYAAKCMAAASSGDS IDMDFSFELFAHVTKFFNYKVVLLGKYNAQGLGSDHELMLRCTKGREYIKVVMQNGRMMGAVLIGETDLEETFENLILNQ MNLSSYGEDLLDPNIDIEDYFD Q8WU10 1.8.1.- MAGNESIUM ION 2.4305e-05 2 MG NICOTINAMIDE-ADENINE-DINUCLEOTIDE 0.0006634249999999999 1 NAD DIHYDROFLAVINE-ADENINE DINUCLEOTIDE 0.000787566 1 FDA singleParticle particle 0.6 8.0 20.0 C8H18N2O4S HEPES 150.0 NaCl Sodium chloride 5.0 MgCl2 Magnesium chloride 0.5 C9H15O6P TCEP 0.5 C21H27N7O14P2 NADH
Dataset 1: 20 mM HEPES pH 8.0, 150 mM NaCl, 0.5 mM TCEP, 5 mM MgCl2 and 0.5 mM NADH, 0.01% Octyl-beta-Glucoside Dataset 2: 20 mM HEPES pH 8.0, 150 mM NaCl, 0.5 mM TCEP, 5 mM MgCl2 and 0.5 mM NADH
 ETHANE 80 277.15 FEI VITROBOT MARK IV
The complex was purified over size exclusion chromatography, prior to grid freezing. Protein concentration per dataset: Dataset 1: 1.5 mg/ ml Dataset 2: 0.6 mg/ ml
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 1.0 2.4 130000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 (6k x 4k) 1 5114 64.592 GATAN K3 (6k x 4k) 1 9302 66.459 1 cryoSPARC 2.3.3 PHASE FLIPPING AND AMPLITUDE CORRECTION C1 3.3 FSC 0.143 CUT-OFF cryoSPARC 3.3.2 288325 MAXIMUM LIKELIHOOD cryoSPARC 2.3.3 MAXIMUM LIKELIHOOD 1 emd_17127.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 288 288 288 0 0 0 288 288 288 187.2 187.2 187.2 90.0 90.0 90.0 X Y Z -0.08911497 0.17467375 -0.0001379971 0.0072747846 0.65 0.65 0.65 0.0289 AUTHOR Unsharpened map emd_17127_msk_1.map emd_17127_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 288 288 288 0 0 0 288 288 288 187.2 187.2 187.2 90.0 90.0 90.0 X Y Z -0.50140953 0.636392 -0.0001379971 0.020280603 0.65 0.65 0.65 AUTHOR Unsharpened map emd_17127_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 288 288 288 0 0 0 288 288 288 187.2 187.2 187.2 90.0 90.0 90.0 X Y Z -0.1543156 0.22951946 0.00021402838 0.015586842 0.65 0.65 0.65 AUTHOR Unsharpened map emd_17127_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 288 288 288 0 0 0 288 288 288 187.2 187.2 187.2 90.0 90.0 90.0 X Y Z -0.1491956 0.21862562 0.00021785569 0.015488094 0.65 0.65 0.65 AUTHOR Unsharpened map