9E6Q
Cryo-em structure of the pyrobaculum calidifontis 50s ribosomal subunit in complex with dri
PDB DOI: 10.2210/pdb9e6q/pdb
Classification: RIBOSOME Organism(s): Pyrobaculum Calidifontis Jcm 11548
Deposited: 2024-10-30 Deposition Author(s): Cate, J.H.D. , Nissley, A.J.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 1.95 Å
Cryo-em structure of the pyrobaculum calidifontis 50s ribosomal subunit in complex with dri
Primary Citation of Related Structures: 9E6Q
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 23S rRNA | 1 | 3024 | NA | UAGGCAAAGCCGCCCGGUGGAUGGCUCGGCUCGGGCGCCGAAGAAGGGCGUGGCAAGCUGCGAUAAGCCCGGGGUAGCCGCAGGCAGGCUUAGAACCCGGGAUCCCCGAAUGGGGCUUCCUGCCGGGGCCGAAUAGGCCCCGGCGCCCCGUAAGGGGCGGGAACGCGGGGAAAGGAAACAUCUUAGUACCCGCAGGAAGGGAAGCCAACAGGGACCCCCUGAGUAGGGGCGACCGAAAGGGGGAUAGCCCAAACCAAAUCCUCGCGGGACAACCGUGGGGAGAUGUGGGGCUUGGGCCCGGGCAACCGCCGGCGGGCGGUAGCCGAAGUGGGCUGGAAUGCCCCGCCGUAGAGGGUGAUAGCCCCGUAGGCGAAACCGCCCGUGGCGGAGUCCCGGGGUCCCGGAGUACCUCGGCUUAGUUUUGCCGGGGGAACGCGCCGGCCACUGGCCGGCAAGGCUAAGCACGUCCCGAGUCCGAUAGCGCACUAGUACCGUGAGGGAAAGCUGAAAAGAACCCCGGAAGGGGGGUGAAAAGAGCCUGAAACCGGGCGGCUACAGUGGGGCAGGCCCGAAAGGAUGCCCCCUCCCGAAGGAAACCCCGGUGACGGGGGAGUACGAGGGAGGGGGUCCAGGGUCUGCCCUUACGUCUAGAAACACGGGCCGGGGAGUUCACGGCCGUGGCGAGCCUAAGGGGUUCAACCCCGGAGGCGUAGGGAAACCGACAGCCCGCAGCGGGGCAACCCGCGAGGGGCGGGGUCUUAAAGGGCCCGUAGUCACGGCCGUGAGACCAGAAACCGGGCGAUCUAGCCCUGGGCAGGGUGAAGCGGGGCGAAAGCCCCGUGGAGGCCCGAAGGGGUUCUGAUGUGCAAAUCGUUCCCAUGACCUGGGGCUAGGGGCAAAAGACCAAUCAAGCCCGGUGAUAGCUGGUUCCCCCCGAAGCGGGUCUCAGCCCGGCCUCCCCGGAGGCGGCCGGCGGGGUAGAGUACUGAUCGGGGGUGCGGGAGCCGAAAGGCUCCGGCCCCCGGUCAAACUCCGAACCUGCCAGCGCCGUAGAAGGGGGGAGGCGGGGGCGGUGGGGUAAGCCUCCGCUCCGAGACGGGAACAACCGAGACCGGGGUUAAGGCCCCCAAGUGCGGGCUUAGUGUCAAUCUAAAAGGGCGUCCCCCGCCCAAGACAGCGGGGCCGUGGGCCUAACAGCAGCCAUCGGCUAAGCAACGCGUAACAGCGGACCCGCCGAGGCGGGGGGCCCCGAAGAUGUACAGGGACUAAGCCCGCCGCCGAGACCCCGGCCCGCGGGCCGUUGGCCCGCGUGGGGUAGGGGGGCGCGGCCGUGGGGCAGAAGCCGGGCCGUGAGGUCCGGUGGACCCGCGGCCGACGAAGAUCCCGGCGGUAGUAGCAGCGAAGAGGGGUGAGAAGCCCCUCCGCCGGAAAGGACCAGGGUUUCCUGGCAACUUCAAUAGGCCAGGAGUUAGCCGGUCCUAAGGCGGGGCCUAAUAGGCACCCGCCGAAAGGGAAACGGGUUAAUAUUCCCGUGCCGCGGGGGUAGGUUCUGCGGCAACGCAGGCCCCGUCCCCGACGCCUCGGGAUAGGGCGGGCGGGACUGCCGUCCCGCUUAACCGUCGAAGGCCGGGGAGUGCCGUAAUGGCGAGAACCGGCCGAAGGCGGGAAUAGCCGGGGGUUUCCCCGGUCCGCCCGACUCCUGGGGCCCGUGAAAAGGGGACGGGGAACGAGCCCCCGCGCCCGUACCGAGAACCGACGCAGGUGCUCCUGGGUGAGAAGCCCAAGGCGGCUCGGGUGACCCCGGGCCAGGGAACUCGGCAAAUUGGCCCCGUAACUUCGGGAGAAGGGGUGCCUGCGGUCUUGGGGUAUACCCCCGGGACCGCAGGUCGCAGUGGCAAGGGGGACCUGACUGUUUAACAAAAACAUAGGUCCCCGCGAGCCCGUAAGGGUGUGUACGGGGGCUGAAUCCUGGCCACUGGCGGUACGUGAACCCCGGGUACAACCGGGCGAAGCGCNGCUGAAGGCCGGGGGUAACUCUGACCCUCUUAAGGUAGCCAAAUGCCUUGCCGGGUAAGUUCCGGCGUGCAUGAAUGGAUCAACGAGGUCCCCACUGUCCCGGCCCGGGGCCCGGCGAACCCACCUCCAGGUGCACAGUCCUGGGACCCCCGACGGGGCGAGAAGUCCCUAUGGAGCUUCACAGCAGCCUGUCGUUGCGGGGGGGCGGGGGGUGCAGAGCGUAGGUGGGAGCGAUGAAACGGGGUCUCCGGGCCCCGUGGAUGCGACCCUGGAACACCACCCACUCUCCGCCCCUCCGCUUACCCGCCGCAAGGCGGGGACAGCGGCAGGCGGGCUGUUCGGCUGGGGCGGCACACCCCUGAAAAGAUAUCGGGGGUGCCCAAAGCUCGGCUCAGGCGGGUCAGAAAUCCGCCGUAGAGUGUAAGGGCAAAAGCCGGGCUGACUGGGCCCUUGAACGCAAGGGGCCCAGGCGGGAAACCGGGGCCUAGAGAACGCUCGUGCCCCCACCAGUGGGGGCCGGGCAUGACAGAAAAGUUACCCUAGGAAUAACCGGCUCGUCGCGGGUGAGAGUCCCCAUCGACCCCGCGGUUUGGUACCCAGACGUCGUCUCUUCCCAUCCUGGCGGUGCAGCAGCCGCCAAGGGUGGGGCUGCCCGCCCAUUAAAGGGGAACGUGAGAUGGGUUCAGACCGUCGCGAGACAGGUCGGUCUCUACCUGUCGGGGGCGCUGGCCGCCUGAGGGGAAGGUGCCCUCAGUACGAGAGGAACGGGGCGCCGCGGCCUCUAGUGUACCGGUUGUCCGGCAGGGCACUGCCGGGCAGCCACGCCGUGGGGGAUAACCGCUGAAAGCAUCUAAGCGGGAAGCCCUCCCCGAGACGAGGCGGCCGUUGCCCUGGGGGCAACCCCGGGGCACGAGGGCUCCCGUAGAAGACGGGGUUGAUGGGGGGGCGGUGUAACCCCCGAGGGUUUCCCGAGGGGAGAGCCGGCCCCUCCCAAUCGCCCGAGCGUGC |
| 5S rRNA | 2 | 129 | NA | GCCCCUAACCCGGCCAUAGGCGCCGGUGCUACACCCGGUCUCAUCAGAACCCGGAAGUUAAGGCCGGCGCCGCGCUCGGGAGUACUGGGCUCCGCGAGGGCCCGGGAAACCGGCGUGCUGGGAGGGGGC |
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| Large ribosomal subunit protein eL40 | AG | 53 | Pyrobaculum Calidifontis Jcm 11548 | MPITLDPEKLAIVLQHRFNYKICRNCGARNPPDAEKCRRCRSRNLRPKKFKKK |
| eL42 | AH | 91 | Pyrobaculum Calidifontis Jcm 11548 | MKFPKSVNMYCPRCNTYTQHSVSNYHGGQRRSLAEGQRRYERKLKGYGSTPKPKQKRFAKVNKKVTLVFTCTKCGYKIVKSLGRMKKVELV |
| Large ribosomal subunit protein eL43 | AI | 102 | Pyrobaculum Calidifontis Jcm 11548 | MPFSHTKIVGPAGRYGARYGMGIRRKVTTIEVKQRGKHRCPSCRSLVRLERLAFGIWHCPKCGHTFAGGAYVPQTILGKTIAPEELKGVEAEKAKWKEAAKR |
| DJ-1/PfpI domain-containing protein | AJ | 184 | Pyrobaculum Calidifontis Jcm 11548 | MPKALLYVIDTAKRDEYPTLKNFLVKGGYEVDVAVGSRDVNVNYTVDLMTLPSDKLPTLFEEYDAFALAGGFKIYYHVLQKKPPLKIWDLNIDKERLAQLVVEFNRRRKLLIAPMAVPAYVAQLGLLSGRHATVYPVTELIKILRDNKVNFVNKQVVRSENIITVKDITTTSEKEFLAALREKG |
| PaREP1 domain containing protein | AK | 93 | Pyrobaculum Calidifontis Jcm 11548 | MPLCSKWESLITWAEKGGNSYKALEFREKLVECIVYTATEKVKKKKLDEAEELLKYGKEVAKKFNIEELNFHIALLEKEISKIRQRRAQAQTK |
| Large ribosomal subunit protein uL15 | AL | 156 | Pyrobaculum Calidifontis Jcm 11548 | MVRRFKRATKYRRGSRTHGWGRVGQHRKSGGSGGKGMVGFHKHKWSLVMKYGESGTGWPFYGKHGFKQPETISVEWRPINVGRLAELVKELRERGEVREEEGRLVVDLLKLGYNKLLGGGHMDVPLVVYTPVASKAAVEKIAKAGGEVRIVSLVHR |
| 50S ribosomal protein L15e | AM | 189 | Pyrobaculum Calidifontis Jcm 11548 | MPSAYQYMAMWYRKVGREVHERLMRSVLIKWRKEPAIVRVERPFRLERARKLGYKPKQGVVVARVRLIRGPFNRRRPDSGRRPKRMGVYGITAWKSWRQVAEERAARKFPGLEVLNSYWVADDGIYRYFEVILIDCNQPTIQRDPLYSGICGREVPRRRLARRLRERQRKLIEHLKKTLLPKLKGTSTA |
| Large ribosomal subunit protein uL16 | AN | 178 | Pyrobaculum Calidifontis Jcm 11548 | MPARPARCYRRIKGPPYTREEYIHGAPMIQIPKFDMGTTSAAARAAFTMVAKLVAEERGQIRMQALEAARQISSKYLTKYVGDANYYLRLNVVPHHVLRENRMLAMAGADRLQEGMRLAFGSPAGRAARVEPGQVIFYVEFKPEHLAHVKEALRRAASKLPIPTRIVVEPKGDGKTAS |
| Large ribosomal subunit protein uL18 | AO | 205 | Pyrobaculum Calidifontis Jcm 11548 | MARGARYKVPFRRRREGVTNYRKRRKLLLSRKPRLVVRKTNKHLIAQIVIARPHGDETVVGLDTRVLSKFGWKGDENNTSAAYLLGLIVGYKARAKGIKEAILDIGLHRPTPGARVFAVMKGVIDAGVEVPHGEEVVPSEERIRGEHVAEYAKRLKEEAPEAYKARFSRYLQRGLPPEELPSHFEEVKKKIVEYYEQKLAKAVAR |
| Large ribosomal subunit protein eL18 | AP | 122 | Pyrobaculum Calidifontis Jcm 11548 | MPPNPTGPTNRQLRMLIRFLRKAATANSANIWRAIAELVERPRRSRVVVNVGKLNRVANDGDVVVIPGKLLGGGELKKRVVVAAVSVTPKAWKKVVEAGGEVLTIPELVRRNPKGSGVKIVI |
| Large ribosomal subunit protein eL19 | AQ | 147 | Pyrobaculum Calidifontis Jcm 11548 | MVDVKRLAAEILGVGVSRVKISPEAVGRLEEVVTKDDVRALIDEGLIWAEPEKGNSRGRWRELHEKKKKGRRRGQGSRKGRRLDEEEAWVNKMRVMRRFLNTLKRQGKLDPATWRQLYRMVKGNYFRDLRHLKTYINEHKLTKEPVK |
| Large ribosomal subunit protein eL20 | AR | 78 | Pyrobaculum Calidifontis Jcm 11548 | MPKIYRVVGDTSTGMKFVVEVVGERPYDALEKVYSVLGSRHKLKRTQIRIREVSVVEPSSAKSNEAKMLMVLEKVVRY |
| Large ribosomal subunit protein eL21 | AS | 99 | Pyrobaculum Calidifontis Jcm 11548 | MVKRTHGYRYKSRKLLSKAPRERGMSGLSRLLYEYKPGDKVVIDIDPTFISTAPHRRYQGKVGVVIGTRGRAYVIETYIGDKKKIIITTPEHLRPHLGG |
| Large ribosomal subunit protein uL22 | AT | 184 | Pyrobaculum Calidifontis Jcm 11548 | MPHFHYSLTDEQAAELVFKKYGVRITPEQIAKAYAPEQRMSWKKSVEVARFIKGMTLKQAKAWLEDVVKLKRPIPIKTFKKKQAHHATPWEGWPVAKWPVKVAKRYLQLLENLENNAKFKGLDVERLVIIHAAAHKGIKIPNIMPRAFGRATPFNEETVNVEIVAAELPKEVVPKRYKLNLVKR |
| Large ribosomal subunit protein uL23 | AU | 81 | Pyrobaculum Calidifontis Jcm 11548 | MIKRFVITEKALRLAERENKITIIVERTATKKQIADEVQRLYNVKVEKVNTLITPRGEKKAYVKLAEGYSAMDLLTKLGVL |
| Large ribosomal subunit protein uL24 | AV | 128 | Pyrobaculum Calidifontis Jcm 11548 | MPFTASAQPRKQRLSLYAAPLHLRRKLLNAKLSPELQKKLGVKRLPVRRGDTVLIMRGDFKGVTGKVVKVDLKRVRIFVEGATRTNSRGQTVYYPIHPSKVMIVDVDLSDKARQKLIERRKRGQHGSS |
| Large ribosomal subunit protein eL24 | AW | 62 | Pyrobaculum Calidifontis Jcm 11548 | MKIHKCSFCGADIPPGYGIMYVRSDGTVQRFCSRKCFVSAVKYGRNPRKLAWVRKKKAKTSK |
| Large ribosomal subunit protein uL29 | AX | 79 | Pyrobaculum Calidifontis Jcm 11548 | MSERKLKPKALREMSPEERRELLNQLRAELVKLQTQRSRGFVEKPGRIRQVRRMIARILTIERELAKAGARAEKGGAKA |
| Large ribosomal subunit protein uL30 | AY | 179 | Pyrobaculum Calidifontis Jcm 11548 | MMAATEQKTVYPRYAVIRLRGIPTTPGDIAATLDLLRLRRKFTMVVVVGSPSVMGMIERVNDWVTWGEIDADTLAEVLRKRGRIVGDKPLTLEYLQKWGWNSFEEVALAYISGEIETLACKKDFKAREGQRPPCIPYLKPFFRLHPPRGGLNSVKLHFSVGGDLGYRGPLINDLIKRML |
| Large ribosomal subunit protein eL30 | AZ | 101 | Pyrobaculum Calidifontis Jcm 11548 | MIDIGRELQVAINTGKVIIGLRETKKSLLTGAPKLVIIAANAPRWAREDIEYYAKLAGVPIFTFPGSSIELGAAAKRPHKIMALAVVDPGQSEILKLVEHA |
| Large ribosomal subunit protein uL2 | AA | 244 | Pyrobaculum Calidifontis Jcm 11548 | MGKRILVQRRGRGGSQFRSPSWKRDGPVRYPPNISGRGIVVEILHEPGLNAPVAKIRMENGVEFFNYAAEGLYVGQVIQVGPDAPPAVGNVLPLGKIPEGTMVFNVEKRFGDGGKFARSGGTYALVIGQRPEENKTIVRLPSGRVIEVDARGRATIGIVAGGGRVEKPFVKAGKKYHRARAKSWKYPTVRGKAMSPYAHPHGGGSHQKGGTPVPKTAPPGQKVGFIGSRCTGRGCVRARAQQKQ |
| Putative signal-transduction protein with CBS domains | 3 | 655 | Pyrobaculum Calidifontis Jcm 11548 | MLTREELEKLAEKRVPQFVRDVVEHPPFRVTVNTTLETLAAYLRKFPVDVVPVFKSVFSDEVAGVVYPHTALLLKSKKLDAKVGEFLNQPLVVKESWRIENVAEMLISESKWGAVVVDEEGKFVGVVSLRGLLSALLLREPKAKSVAAVYTSIDEKKPRVGFVKAIEKVSKIFHKLVGGEVDGYVVLNREGGAAGILTVWNFLKSRRWFRGSGEPRAIFGTRVTRGESKPRGVARVWRIMSRGVAVANPDTPITDVARYMATFGIYVVPVVDRNGKVIGAVTAWDVLHAYLYGPKEGREDVEVKTAVEVPVSKPSMEAVIRLKPVKHVTGLRARDVMLSDVPMVNVRDPLSSIRKAFLRSKSGILAVVDDSGKVVGFITRRDFMSYIAEKSLGYWRRQKGKLLVLREEALPGEQAKLAVEEGTAGDLAKSEYPTVSESATLEEVAYKMLAAGTDYVVVIDSAGQPIGVVTKDELVKAYKERGRSVKVGELMTPADVAAVNPFSSLMSTTRKINAFELDGVVVVEGGNIMGVVTVDDLALRPVEETLRGERVVYFTKSGVLRKATTGLSRLRYSKVGTLTALDVSRPVDHVANVNADVKEVLDKLVEQGVVPVVDEQGRLVGVLNKMDIVKDLARVYVTYAMPEKLAEVKQVEERA |
| Large ribosomal subunit protein uL3 | AB | 338 | Pyrobaculum Calidifontis Jcm 11548 | MGLKINRPRRGSMGVYPRKRAADIVPRVRTWPEVNLGKPTLLGFAAYKAGMLHAVVVDDRPTSPLYGKEVVKAVTVLDAPPLYVAAVRLYTLDPTNGYKVAVGEAWVSEPPADLRRVLTLPEKFDTEKQLKALEEYRDVAVDVRVLVATQPRLSGIGKKTPEVLEIPVGGVPSIDERINFAISLLGKTVSPKDVFTPGQLVDVIAVTKGKGYQGVVKRFGVTILPRWHKHRKGHRRTGTIGPQAPALMFTQPRPGQMGFHQRTEYNKRILKIGDNGAEITPKSGFPHYGVIKGPYILLQGSVPGARKRLVVLRYPVRPPKKAPPAAEPQVVWVSSQSI |
| Large ribosomal subunit protein uL4 | AC | 285 | Pyrobaculum Calidifontis Jcm 11548 | MGAVVKELLKFKLLDLSPYIKPAEERPPEALKVYDVNGQYMADIETPIHFYEPVRPDLIRRAYLSALSARFQPKGVYEGAGKEHSCESFGVGLGIARIPRYKGHLWPRGCFAPNTRGGRRAHPPRPEKKLHEEINWKEKNLAIRSAIAATAYKSWVAARGHMVEKVPSLPLVVSGDAEKIAKAKEAKKLFEVLGLWPDVERAAEGVKIRAGKGKMRGRRYKEPKSVLVVVSELDVPLIGAVRNFPGVDVVPVSHLNMLVLAPGGVPGRLTLWTATAVERLKGLFL |
| Large ribosomal subunit protein uL5 | AD | 178 | Pyrobaculum Calidifontis Jcm 11548 | MKWKELVLVKDHPMKRVYIEKVVVNIGVGTGGERLEKAANLLRELTGAEPSLRRAKRSIKDFGIRKGEPIGVAVTLRRDKAVEFLMRALQAVGNRIKRSSFDERGNVCFGIKEHIMLPGVKYDPAVGIWGMDVCVRLAKPGLRVQLRRRRRSKVGKGQLVTREEAVEFFQKVLGVQVD |
| Large ribosomal subunit protein uL6 | AE | 196 | Pyrobaculum Calidifontis Jcm 11548 | MHVVYAVEEVPIPDGVKVAIEKTGPFDYVVKVKGPLGELVKEFKNTPVIMSLSDGKVVLEVLNAKKREYALLGTYKGILKNMFLGVTKGWRYKLKVIYTHFPMLVKVQGNQLTIENFLGRKSKIVLEIPKGVKVEVKGKEDIVVEGIDRELVSQFAAAIQAATELRGEEKPSPHGREGGLGVVDGIYVVGYEHVKA |
| Large ribosomal subunit protein eL8 | AF | 149 | Pyrobaculum Calidifontis Jcm 11548 | MAVTIDPKTFYANPLPGKPFYVRFEVPSDVAEKALEILSIARQTGKIKKGTNETTKAVERGLAKLVLIAEDVDPPEVVAHLPLLCEEKKVPYVYVPSKEKLGKAAGINVAAAAAVVIEAGQAAGELEALVNKINEIRAKHGLNAIPVRR |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2024-10-30 Deposition Author(s): Cate, J.H.D. , Nissley, A.J.