2025-05-14 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY STRUCTURE_SUMMARY em_admin em_imaging em_software entity entity_poly entity_src_gen struct_keywords struct_ref struct_ref_seq struct_ref_seq_dif _em_admin.last_update _em_imaging.microscope_model _entity.formula_weight _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_src_gen.pdbx_end_seq_num _struct_keywords.pdbx_keywords _struct_keywords.text _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.seq_align_beg _struct_ref_seq.seq_align_end COORDINATE_REPLACEMENT AUTHOR Sequence discrepancy
tRNA model had a single nucleotide frame shift due to missing 5' guanosine
STRUCTURE_SUMMARY atom_site atom_site_anisotrop em_admin em_imaging em_software entity entity_poly entity_poly_seq entity_src_gen ndb_struct_na_base_pair ndb_struct_na_base_pair_step pdbx_contact_author pdbx_poly_seq_scheme pdbx_struct_sheet_hbond pdbx_unobs_or_zero_occ_atoms pdbx_unobs_or_zero_occ_residues pdbx_validate_close_contact pdbx_validate_rmsd_angle pdbx_validate_rmsd_bond pdbx_validate_torsion struct_conf struct_conn struct_keywords struct_mon_prot_cis struct_ref struct_ref_seq struct_ref_seq_dif struct_sheet struct_sheet_order struct_sheet_range _em_admin.last_update _em_imaging.microscope_model _entity.formula_weight _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_src_gen.pdbx_end_seq_num _struct_keywords.pdbx_keywords _struct_keywords.text _struct_mon_prot_cis.pdbx_omega_angle _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.seq_align_beg _struct_ref_seq.seq_align_end RCSB RCSB 2023-10-21 2024-12-18 2024-12-18 2025-05-14 Canadian Institutes of Health Research (CIHR) PJT-178026 Canada Structure of the KEOPS complex (Cgi121/Bud32/Kae1/Pcc1) bound to tRNA in its native-like conformation. Ona Chuquimarca SM Beenstock J Daou S Keszei AFA Yin Z Sicheri F tRNA, modification, t6A, RNA BINDING PROTEIN, RNA BINDING PROTEIN-RNA complex Ona Chuquimarca SM Beenstock J Daou S Porat J Keszei AFA Yin JZ Beschauner T Bayfield MA Mazhab-Jafari MT Sicheri F Structures of KEOPS bound to tRNA reveal functional roles of the kinase Bud32. Nat Commun UK 15 10633 10633 2024 39639027 doi:10.1038/s41467-024-54787-w 2041-1723 EMD-42407 other EM volume 8up5 FULLOVERLAP Structure of the KEOPS complex (Cgi121/Bud32/Kae1/Pcc1) bound to tRNA in its native-like conformation. Structure of the KEOPS complex (Cgi121/Bud32/Kae1/Pcc1) bound to tRNA in its native-like conformation. 0 1 2 3 4 5 Methanocaldococcus jannaschii Bud32 1 2 Methanocaldococcus jannaschii Cgi121 1 4 Methanocaldococcus jannaschii Kae1 1 3 Methanocaldococcus jannaschii Pcc1 1 5 Pyrococcus furiosus tRNA 1 1 Methanocaldococcus jannaschii tRNA Methanocaldococcus jannaschii 0.024758672 1 GGGCCCGUAGCUCAGUCUGGCAGAGCGCCUGGCUUUUAACCAGGUGGUCGAGGGUUCAAAUCCCUUCGGGCCCGCCA L77117.1 Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein Methanocaldococcus jannaschii 0.023957547 1 Escherichia coli BL21(DE3) LEVO KIPEHLIGKGAEADIKRDSYLDFDVIIKERVKKGYRDERLDENIRKSRTAREARYLALVKDFGIPAPYIFDVDLDNKRIM MSYINGKLAKDVIEDNLDIAYKIGEIVGKLHKNDVIHNDLTTSNFIFDKDLYIIDFGLGKISNLDRDKAVDLIVFKKAVL STHHEKFDEIWERFLEGYKSVYDRWEIILELMKDVERRARYVE Q58530 Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein Methanocaldococcus jannaschii 0.035869402 1 Escherichia coli BL21(DE3) LEVO PMICLGLEGTAEKTGVGIVTSDGEVLFNKTIMYKPPKQGINPREAADHHAETFPKLIKEAFEVVDKNEIDLIAFSQGPGL GPSLRVTATVARTLSLTLKKPIIGVNHCIAHIEIGKLTTEAEDPLTLYVSGGNTQVIAYVSKKYRVFGETLDIAVGNCLD QFARYVNLPHPGGPYIEELARKGKKLVDLPYTVKGMDIAFSGLLTAAMRAYDAGERLEDICYSLQEYAFSMLTEITERAL AHTNKGEVMLVGGVAANNRLREMLKAMCEGQNVDFYVPPKEFCGDNGAMIAWLGLLMHKNGRWMSLDETKIIPNYRTDMV EVNWI Q58530 Regulatory protein Cgi121 Methanocaldococcus jannaschii 0.016963937999999998 1 Escherichia coli BL21(DE3) LEVO MDPMIIRGIRGARINNEIFNLGLKFQILNADVVATKKHVLHAINQAKTKKPIAKSFWMEILVRASGQRQIHEAIKIIGAK DGNVCLICEDEETFRKIYELIGGEIDDSVLEINEDKERLIREIFKIRGFGNVVERVLEKIALIELKKE A0A832SJR9 KEOPS complex subunit Pcc1 Pyrococcus furiosus DSM 3638 0.019731768 1 Escherichia coli BL21(DE3) LEVO MKAKRVQAKIEIEFPSEDVAKVVYEAVLYEHLSVPYRRSEIDFKLEGKKIILDIKATDSSALRGTVNSYLRWIKAAIDVI EVGSGSGSGSGSGMKAKRVQAKIEIEFPSEDVAKVVYEAVLYEHLSVPYRRSEIDFKLEGKKIILDIKATDSSALRGTVN SYLRWIKYAIDRIEV Q8TZI1 singleParticle particle 7.5 ETHANE TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.4 2.9 GATAN K3 (6k x 4k) 55.61 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 3.56 FSC 0.143 CUT-OFF 121003 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_42443.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 263.68 263.68 263.68 90.0 90.0 90.0 X Y Z -1.5325017 2.7217388 -0.000033373828 0.04682124 1.03 1.03 1.03 0.282 AUTHOR Structure of the KEOPS complex (Cgi121/Bud32/Kae1/Pcc1) bound to tRNA in its native-like conformation emd_42443_msk_1.map emd_42443_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 263.68 263.68 263.68 90.0 90.0 90.0 X Y Z -0.30599064 1.0011929 -0.000033373854 0.030814806 1.03 1.03 1.03 AUTHOR Additional Map emd_42443_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 263.68 263.68 263.68 90.0 90.0 90.0 X Y Z -0.4824919 1.0230913 0.000984518 0.035942268 1.03 1.03 1.03 AUTHOR Half Map B emd_42443_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 263.68 263.68 263.68 90.0 90.0 90.0 X Y Z -0.45147443 1.0645103 0.000981627 0.035939448 1.03 1.03 1.03 AUTHOR Half Map A