Cryo-EM structure of yeast Ribonuclease P with pre-tRNA substrate

2025-09-17 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY database_2 em_admin _database_2.pdbx_DOI _database_2.pdbx_database_accession _em_admin.last_update EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond database_2 em_admin pdbx_entry_details pdbx_struct_conn_angle struct_conn struct_conn_type _database_2.pdbx_DOI _database_2.pdbx_database_accession _em_admin.last_update _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.value _struct_conn.conn_type_id _struct_conn.id _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn_type.id DERIVED_CALCULATIONS em_admin pdbx_validate_close_contact struct_conn _em_admin.last_update PDBj PDBj 2018-08-16 2018-10-17 2018-10-17 2025-09-17 Cryo-EM structure of yeast Ribonuclease P with pre-tRNA substrate Lan P Tan M Ribonuclease P, RNA-protein complex, HYDROLASE-RNA complex Lan P Tan M Zhang Y Niu S Chen J Shi S Qiu S Wang X Peng X Cai G Cheng H Wu J Li G Lei M Structural insight into precursor tRNA processing by yeast ribonuclease P. Science US 362 2018 30262633 doi:10.1126/science.aat6678 1095-9203 0038 SCIEAS EMD-9616 other EM volume 6ah3 FULLOVERLAP EMDB EMD-9616 other EM volume EMDB EMD-9622 associated EM volume

cryo-EM structure of yeast Ribonuclease P with pre-tRNA substrate

RNase P with pre-tRNA substrate RNase P with pre-tRNA substrate 0 1 2 3 4 5 6 7 8 9 10 11 RNase P 1 1 2 3 4 5 6 7 8 9 10 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) pre-tRNA 1 11 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) Ribonuclease P RNA Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.118857781 1 GUGGAACAGUGGUAAUUCCUACGAUUAAGAAACCUGUUUACAGAAGGAUCCCCACCUAUGGGCGGGUUAUCAGAUAUUAU CAGGUGGGAAAUUCGGUGGAACACAGUGGAGCCUUGUCCUCCGGGUUAAUGUCGCUUUUGGCAUUGGCCCCUGCUCCUGA GAGAAGAAAUAUACUGGGGAACCAGUCUUUACCGACCGUUGUUAUCAGAAAUUCACGGAGUUCGGCCUAGGUCGGACUCC GAUGGGAACGGCAACGGUUGUUCCGUUUGACUUGUCGCCCGCUACGGCGUGAGCGUCAAGGUCUGUUGAGUGCAAUCGUA GGACGUCAUUAGUGGCGAACCCGAUACCGAUUACUGCUGCUGUUCCAGC CP020127.1 Ribonucleases P/MRP protein subunit POP1 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.100559555 1 LEVO MSGSLSRGNGGKKVLNKNQLLKRNRIRNARSIRAEAVAASSTKTGTPSDLSESGSKLNVDQFISSRQFEVKQLQLAMHNS KAASSTRIFQALPRKLRRRTASHNVRRIPKRMRNRALREMRKSDQQDVLKGSSASSRKAHGLNAKQLYKARMSIKLLRLA SKSTSMKLSMPPEVTSSNCHVRQKIKTLKRMIKESSTANPNIKLLNNRMGSYDCTGVNELAPIPKGRVKYTKRQKHFAWL PTHIWNAKRSHMMKRWGYQMVWAPTQKCFKLTHRLGGDTCSSDGALCMDSSYIGTIIVKDKSNDSEGDFLKSIIGKLTAE RANLRKYREGQVLFQGLIYSFNEENGEDSTKPLGPCDVFWVQKDTAIIRLHPSIYTQVFNILLQHKEKLTVQDCRYSLAS VTLKGAKALESLASCLRSTEYSKSFEQFKMVSMITDHNALPQRCTFAFEAIDPRHLAAPKKLNDSQRKTVNSDDILSLHE NYPQDEINAVFNELCDPESRTQSYNNQNTLKEISARRYKLLTATPNSINKTTVPFKESDDPSIPLVIIRRLKTRDWIVVL PWFWLLPLWHLLNRIPRMYHIGLRQFQQIQYENKQLYFPDDYPFTQLGYIENSFYKKEASKTKWDRKPMGKRINFEKIKD IHNTKLPAYSGEIGDFFSSDWRFLQILRNGIDYLQRNDKTLELMDSKKTGQFNAQGVRDINCVNDVLEFCKDYEAKTKAM SLSIEENIPVALCKNRKCQFRTPDSISVNSSSFSLTFFPRCIIAVSCTLLERGHPKDNARIYQVPEKDLEHWLQLAKGVY RPNGRKDHDLKIPLPEVHDLIGFITSGTYHLNCGNGMGIGFIDHHAAIRQPTRYVLIRNVGTNTYRLGEWSKISV P41812 3.1.26.5 Ribonucleases P/MRP protein subunit POP3 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.022643721000000002 1 LEVO MSGSLKSLDKKIAKRRQVYKPVLDNPFTNEAHMWPRVHDQPLIWQLLQSSIINKLIHIQSKENYPWELYTDFNEIVQYLS GAHGNSDPVCLFVCNKDPDVPLVLLQQIPLLCYMAPMTVKLVQLPKSAMDTFKSVSKYGMLLLRCDDRVDKKFVSQIQKN VDLLQFPWLNAIKYRPTSVKLLKTTVPIVSKKRQK P53833 RNases MRP/P 32.9 kDa subunit Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.032933168 1 LEVO MDRTQTFIKDCLFTKCLEDPEKPFNENRFQDTLLLLPTDGGLTSRLQRQQRKSKLNLDNLQKVSQLESADKQLEKRDYQR INKNSKIALREYINNCKKNTKKCLKLAYENKITDKEDLLHYIEEKHPTIYESLPQYVDFVPMYKELWINYIKELLNITKN LKTFNGSLALLKLSMADYNGALLRVTKSKNKTLIGLQGIVIWDSQKFFIMIVKGNIIDEIKCIPKKGTVFQFEIPISDDD DSALRYSILGDRFKYRSVDRAGRKFKSRRCDDMLYYIQN P38336 Ribonuclease P/MRP protein subunit POP5 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.01960159 1 LEVO MVRLKSRYILFEIIFPPTDTNVEESVSKADILLSHHRASPADVSIKSILQEIRRSLSLNLGDYGSAKCNSLLQLKYFSNK TSTGIIRCHREDCDLVIMALMLMSKIGDVDGLIVNPVKVSGTIKKIEQFAMRRNSKILNIIKCSQSSHLSDNDFIINDFK KIGRENENENEDD P28005 3.1.26.5 Ribonucleases P/MRP protein subunit POP6 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.018234959 1 LEVO MINGVYYNEISRDLDISSSTQCLRFLKETVIPSLANNGNNSTSIQYHGISKNDNIKKSVNKLDKQINMADRSLGLQQVVC IFSYGPHIQKMLSILEIFKKGYIKNNKKIYQWNKLTSFDIKREGRNELQEERLKVPILVTLVSDSEIIDLNLHSFTKQ P53218 3.1.26.5 Ribonucleases P/MRP protein subunit POP7 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.015844284 1 LEVO MALKKNTHNKSTKRVTKHPSLKTLTHKQIHTTIFVKSTTPYVSALKRINKFLDSVHKQGSSYVAVLGMGKAVEKTLALGC HFQDQKNKKIEVYTKTIEVLDEVITEGQADIDMESDVEDDDKETQLKKRAVSGVELRIYV P38291 3.1.26.5 Ribonucleases P/MRP protein subunit POP8 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.015530351 1 LEVO MGKKTFREWQYFKLSITSFDQDVDDAHAIDQMTWRQWLNNALKRSYGIFGEGVEYSFLHVDDKLAYIRVNHADKDTFSSS ISTYISTDELVGSPLTVSILQESSSLRLLEVTDDDRLWLKKVMEEEEQDCKCI P38208 3.1.26.5 Ribonuclease P/MRP protein subunit RPP1 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.032270261999999994 2 LEVO MLVDLNVPWPQNSYADKVTSQAVNNLIKTLSTLHMLGYTHIAINFTVNHSEKFPNDVKLLNPIDIKRRFGELMDRTGLKL YSRITLIIDDPSKGQSLSKISQAFDIVAALPISEKGLTLSTTNLDIDLLTFQYGSRLPTFLKHKSICSCVNRGVKLEIVY GYALRDVQARRQFVSNVRSVIRSSRSRGIVIGSGAMSPLECRNILGVTSLIKNLGLPSDRCSKAMGDLASLVLLNGRLRN KSHKQTIVTGGGSGNGDDVVNDVQGIDDVQTIKVVKRSMDAEQLGHASKRHKP P38786 3.1.26.5 Ribonuclease P protein subunit RPR2 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.016375049 1 LEVO MGKKAHGGKMKPEIDENGTLLVPPPRTIANQDHFHRLNYLYQISAYQTRARQKARTDAHTPLARNYIKSMDLISKKTKTS LLPTIKRTICKKCHRLLWTPKKLEITSDGALSVMCGCGTVKRFNIGADPNYRTYSEREGNLLNS P40571 3.1.26.5 pre-tRNA Saccharomyces cerevisiae S288c 0.025830323999999998 1 AGAAGCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUCUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCAUUU MAGNESIUM ION 2.4305e-05 2 MG ZINC ION 6.5409e-05 1 ZN singleParticle particle 7.5 ETHANE FEI TITAN KRIOS OTHER BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K2 SUMMIT (4k x 4k) 1.5625 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 3.48 FSC 0.143 CUT-OFF 176896 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_9622.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 337.92 337.92 337.92 90.0 90.0 90.0 X Y Z -0.1938393 0.30816835 0.00026609402 0.0092275115 1.32 1.32 1.32 0.025 AUTHOR ::::EMDATABANK.org::::EMD-9622::::