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7QIW

Specific features and methylation sites of a plant ribosome. 60s ribosomal subunit.

PDB DOI: 10.2210/pdb7qiw/pdb

Classification: RIBOSOME
Organism(s): Solanum Lycopersicum

Deposited: 2021-12-16
Deposition Author(s): Amunts, A. , Cottilli, P. , Itoh, Y.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.35 Å

7qiw
Literature

Specific features and methylation sites of a plant ribosome. 60s ribosomal subunit.

Amunts, A. , Cottilli, P. , Itoh, Y.

Primary Citation of Related Structures: 7QIW


Proteins
Molecule Chains Sequence Length Organism Sequence
60S ribosomal protein L29 D 60 Solanum Lycopersicum MAKSKNHTAHNQSYKAHRNGIKKPKSHRHSSTKGMDPKFLRNQRYARKHNKKNGETAAEE
60S ribosomal protein L38 M 69 Solanum Lycopersicum MPKQIHEIKDFLLTARRKDARTVKIKKNKDMVKFKVRCSKYLYTLCVSDFEKADKLKQSLPPGLSVQDL
60S ribosomal protein eL39 N 51 Solanum Lycopersicum MPSHKSFMIKKKLAKKQRQNRPIPYWIRMRTDNTIRYNAKRRHWRRTKLGF
Ubiquitin-like domain-containing protein O 128 Solanum Lycopersicum MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIEPSLMALARKYNQEKMICRKCYARLHPRAVNCRKRKCGHSNQLRPKKKIK
60S ribosomal protein eL42 P 105 Solanum Lycopersicum MVNVPKTKKTYCKSKECKKHTLHKVTQYKKGKDSLAAQGKRRYDRKQSGYGGQTKPVFHKKAKTTKKIVLRLQCQGCKHVSQHPIKRCKHFEIGGDKKGKGTSLF
60S ribosomal protein eL43 Q 92 Solanum Lycopersicum MTKRTKKAGIVGKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDCGKVKAGGAYTLNTASAVTVRSTIRRLREQTES
Ribosomal_L28e domain-containing protein R 143 Solanum Lycopersicum MTTVPGQLVWEIVKKNNSFLVKEFGNGTAGVVFSKEPNNLYNLHSYKHSGLANKKTVTIQPDGKDKSVLLATSKTKKQNKPSRLLNKSVMKKEFSRMAKAVTNQVGDNYYRPDLKKAALARLSAVHRSLKVTKSGAKKRNRQA
Ribosomal protein L19 T 213 Solanum Lycopersicum MVSLKLQKRLAASVLKCGRGKVWLDPNEGNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGKRKGTREARLPTKVLWMRRLRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMENIHKTKAEKAREKTLSDQFEARRAKNKASRERKFARRKKRLAQGPGGEKPVQPAAPAAAAPAQPAQGSKKSKK
60S ribosomal protein L18a U 178 Solanum Lycopersicum MVTYKFHQYQVVGRALPSENDEHPKIYRMKLWATNEVRAKSKFWYFLRKLKKVKKSNGQMLAINEIFEKYPTTIKNYGIWLRYQSRTGYHNMYKEYRDTTLNGAVEQMYTEMASRHRVRHHCIQIIKTATIPAKLCKRESTKQFHDSKIKFPLVFKKVRPPSRKLKTTYKATKPNLFM
60S ribosomal protein eL21 V 164 Solanum Lycopersicum MPAGHGLRSRTRDSFSRAFRKKGTIALSTYLRIFKIGDYVDIKVNGAIHKGMPHKFYHGRTGRVWNVTKRAVGVEVNKQVRNKILRKRIHVRIEHVQQSRCTEEVRERIKKNDQLKADAKARGEVISTKRQPLGPKPGFMVEGATLETVTPIPYDVVNDLKGGY
60S ribosomal protein eL31 F 120 Solanum Lycopersicum MVEKTKGRKEEVVSREYTINLHKRLHGCTFKKKAPTAIKEIRKFAQKAMGTKDVRVDVKLNKQIWSRGIRSVPRRVRVRIARKRNDDEDAKEELYSLVTVAEIPAEGLKGLGTKIIEDEE
60S ribosomal protein eL22 W 124 Solanum Lycopersicum MSRAAAAVKGGKKKGASFVIDCSKPVEDSIMEIASLDKFLQERIKVGGKAGALGDSVTVTRDKNKITVTCNSTFSKRYLKYLVKKYLKKNNVRDWLRVIASNKDRNVYELRYFNIAENEADEED
60S ribosomal protein uL14 X 140 Solanum Lycopersicum MSKRGRGGSAGNKFRMSLGLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPDLRKKVMPAVIVRQRKPWRRKDGVFMYFEDNAGVIVNPKGEMKGSAITGPIGKECADLWPRIASAANAIV
TRASH domain-containing protein Y 165 Solanum Lycopersicum MMVLKTELCRFSGAKIYPGRGIRFIRSDSQVFLFVNSKCKHYFHNKLKPSKLTWTAMYRKQHKKDIAQEAAKKRRRTTKKPYSRSIVGATLEVIQKKRTERPEVRDAAREAALREIKERIKKTKDEKKAKKAEVQAKSQKAGGKGNMSKGGASKGPKLGGGGGKR
Ribosomal_L23eN domain-containing protein Z 154 Solanum Lycopersicum MAPAKVDLTKKKDPKAQAVKAAKAVKSGSTFKKKSSKIRTKVTFHRPKTLKKDRSPKYPRVSAPGRNRLDQYAILKYPLTTESAMKKIEDNNTLVFIVDIKADKKKIKDAVKKMYDIQIKKVNTLIRPDGTKKAYVRLTPDYDALDVANKIGII
KOW domain-containing protein A 146 Solanum Lycopersicum MKYNPRVSSSRRKSRKAHFTAPSSVRRVLMSAPLSSELRAKYNVRSMPVRKDDEVQVVRGTYKGREGKVVQVYRKKWVIHIERITREKVNGSTVNVGINPSKVVVSKLRLDKDRRSLLDRKAKGRAAADKDKGTKFTTEEIMQAID
60S ribosomal protein L27 B 135 Solanum Lycopersicum MVKFLKPNKAVILLQGKYAGRKAVIVRAFDEGTRDRPYGHCLVAGISKYPKKVIRKDSAKKQAKKSRVKAFIKLVNYNHIMPTRYTLDVDLKDVVNADVLQARDKKVTAAKETKARFEERFKTGKNRWFFTKLRF
Putative 60S ribosomal protein L27a-3-like C 148 Solanum Lycopersicum MTTRFKKNRKKRGHVSAGHGRIGKHRKHPGGRGNAGGMHHHRILFDKYHPGYFGKVGMRYFHKLRNKFYCPTVNIDTLWSLVPQEVKDKAAANKGTAPLIDVTQFGYFKVLGKGVLPTGQPVVVKAKLISKNAEKKIKENGGAVVLTA
Ribosomal protein L3 E 389 Solanum Lycopersicum MSHRKFEHPRHGSLGFLPRKRAARHRGKVKAFPKDDPSKPCKLTAFLGYKAGMTHIVREVEKPGSKLHKKETCEAVTIVETPPMVIVGVVGYVKTPRGLRCLNTVWAQHLSEDIKRRFYKNWCKSKKKAFLKYSKKYETDEGKKDIQAQLEKLKKYACVIRVLAHTQIRKMKGLKQKKAHLMEIQVNGGSIAQKVDFAYGFFEKQVPVDAVFQKDEMIDIIGVTKGKGYEGVVTRWGVTRLPRKTHRGLRKVACIGAWHPARVSFTVARAGQNGYHHRTEMNKKVYKLGKVGQESHTALTEFDRTEKDITPIGGFPHYGVVKEDYLLIKGCCVGTKKRVVTLRQSLLNQTSRVALEEIKLKFIDTSSKFGHGRFQTTQEKQKFYGRLKA
Ribosomal_L18_c domain-containing protein G 301 Solanum Lycopersicum MAFIKVQKTRAYFKRFQVKFKRRREGKTDYRARNRLINQDKNKYNTPKYRFVVRFTNKDIIAQIVSASIAGDMILASAYANELPHYGLEVGLTNYAAAYCTGLLLARRVLKKLEMDEEYEGNLEVNGEDYSVEPAESRRPFRALLDVGLLRTTTGNRVFGALKGALDGGLDIPHSEKRFAGFSKDSKQLDADVHRKYIYGGHVATYMQTLIEDEPEKYQTHFSQYIKKGFEADGLEEMYKKVHAAIRADPSPKKSEKQPPKQHKRYNLKKLTYEERKAKLIERLNALNSAAGNDDDDEDDE
Ribosomal_L6e_N domain-containing protein H 229 Solanum Lycopersicum MAAKKTIRNPELIRGVGKFSRSKMYHKKGLWAIKKKNGGKLPLHEKKPAVAVAAVKPPKFYPADDVKKPLVNKHKPKPTKLRASITPGTVLIILAGRFKGKRVVFLKQLTSGLLLVTGPFKLNGVPLRRVNQAYVIGTSTKVDVSGVNVEKIDDKYFAKQVEKKQKKGEGEFFEDKKEEKNVLPQEKKDEQKTVDSALLKAIEGIPELKAYLSARFSLKSGMKPHELVF
Thaliana 60S ribosomal protein L7 I 242 Solanum Lycopersicum MGEGGVVVPESVLKKQKRNEEWALVKKQELAVAKKKSVENRKLIYNRAKQYAKEYSEQEKELIRLKREARLKGGFYVDPEAKLLFIIRIRGINAMPPQTKKILQLLRLRQIFNGVFLKVNKATVNMLHRVEPYVTYGYPNLKSIKELIYKRGYGKVDKQRIALTDNAVVEQVLGKHGIICIEDLVHEIITVGPHFKEANNFLWPFQLKAPLGGLKKKRNHYVEGGDAGNRENFINELIRRMN
Ribosomal_L7Ae domain-containing protein J 258 Solanum Lycopersicum MAPKKGVAVSAKKKPEKAKVLNPLFEKRPKQFGIGGALPPKKDVTRNVRWPRNVTLQRKKRILKMRLKVPPALNQFTKTLDKNLATTLFKMLLKYRPEDKAAKKERLVKRAQAEAEGKTPETKKPIIVKYGLKHITYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKARLGSIVHKKTASALCLTTVKNEDKMEFSRVLEAIKANFNDKYEENRKKWGGGIMGSKSQARTKAKERVLAKEAAQRLN
60S ribosomal protein uL6 K 194 Solanum Lycopersicum MKTILSSETMDIPDGITIKVKAKQIEVEGPRGKLTRNFKHLNLDFQLIKDEETGKKKLKIDAWFGSRKTTAAIRTALSHVENLITGVTKGYRYKMRFVYAHFPINASISGGNKSIEIRNFLGEKKVRKVDMLDGVTVVRSEKVKDELVLDGNDIELVSRSAALINQKCHVKNKDIRKFLDGIYVSEKGRIAEEE
60S ribosomal protein L10 L 220 Solanum Lycopersicum MGRRPARCYRQIKNKPYPKSRFCRGVPDPKIRIYDVGMKKKGVDEFPFCVHLVSWEKENVSSEALEAARIACNKYMTKSAGKDAFHLRVRVHPFHVLRINKMLSCAGADRLQTGMRGAFGKPQGVCARVAIGQVLLSVRCKDGNANHAQEALRRAKFKFPGRQKIIVSRKWGFTKFSRTDYLKYKSENRIVPDGVNAKLLGCHGRLAARQPGRAFLEAAN

Nucleic Acids / Hybrid
Molecule Chains Sequence Length Organism Sequence
tRNA s 2 NA CA
25S rRNA 2 3391 NA GCGACCCCAGGUCAGGCGGGAUUACCCGCUGAGUUUAAGCAUAUCAAUAAGCGGAGGAAAAGAAACUUACAAGGAUUCCCCUAGUAACGGCGAGCGAACCGGGAACAGCCCAGCCUUAGAAUCGGGCGGCUCCGUCGUCCGAAUUGUAGUCUGGAGAAGCGUCCUCAGCGGCGGACCGGGCCCAAGUCCCCUGGAAGGGGGCGCCGGAGAGGGUGAGAGCCCCGUCGUGCCCGGACCCUGUCGCACCACGAGGCGCUGUCUACGAGUCGGGUUGUUUGGGAAUGCAGCCCAAAUCGGGCGGUGAAUUCCGUCCAAGGCUAAAUACUGGCGAGAGACCGAUAGCGAACAAGUACCGCGAGGGAAAGAUGAAAAGGACUUUGAAAAGAGAGUCAAAGAGUGCUUGAAAUUGUCGGGAGGGAAGCGGAUGGGGGCCGGCGAUGCGCCCCGGUCGGAUGUGGAACGGCGACGAGCCGGUCCGCCGAUCGACUCGGGGCGUGGACCAGCGUGGAUUGGGGGGGCGGCCAAAGCCCGGGCUCUCGAUACGCCCGUGGAACGCCGUCUCCCCGAUUGUGGAAGGCAGCGCGCGCCUCCGGCGUGCUUCGGCAUCUGCGCGCUCCGGACGCUGGCCUGUGGGCUCCCCAUUCGACCCGUCUUGAAACACGGACCAAGGAGUCUGACAUGUGUGCGAGUCAACGGGCGAGUAAACCCGUAAGGCGUAAGGAAGCUGAUUGGUGGGAUCCCCCUGAGGGGUGCACCGCCGACCGACCUUGAUCUUCUGAGAAGGGUUCGAGUGUGAGCAUACCUGUCGGGACCCGAAAGAUGGUGAACUAUGCCUGAGCGGGGCGAAGCCAGAGGAAACUCUGGUGGAGGCCCGCAGCGAUACUGACGUGCAAAUCGUUCGUCUGACUUGGGUAUAGGGGCGAAAGACUAAUCGAACCGUCUAGUAGCUGGUUCCCUCCGAAGUUUCCCUCAGGAUAGCUGGAGCUCGCGUGCGAGUUCUAUCGGGUAAAGCCAAUGAUUAGAGGCCUCGGGGGCGCAACGCCCUCGACCUAUUCUCAAACUUUAAAUAGGUAGGACGGCGCGGCUGCUUUGUUGAGCCGCGCCACGGAAUCAAGAGCUCCAAGUGGGCCAUUUUUGGUAAGCAGAACUGGCGAUGCGGGAUGAACCGGAAGCCGGGUUACGGUGCCAAACUGCGCGCUAACCUAGAUCCCACAAAGGGUGUUGGUCGAUUAAGACAGCAGGACGGUGGUCAUGGAAGUCGAAAUCCGCUAAGGAGUGUGUAACAACUCACCUGCCGAAUCAACUAGCCCCGAAAAUGGAUGGCGCUUAAGCGCGCGACCUACACCCGGCCGUCGGGGCAAGUGCCAGGCCCCGAUGAGUAGGAGGGCGCGGCGGUCGCUGCAAAACCUUGGGCGCGAGCCUGGGCGGAGCGGCCGUCGGUGCAGAUCUUGGUGGUAGUAGCAAAUAUUCAAAUGAGAACUUUGAAGGCCGAAGAGGGGAAAGGUUCCAUGUGAACGGCACUUGCACAUGGGUUAGUCGAUCCUAAGGGUCGGGGGAACCCCGACAGAUAGCGCGUUUCGCGCGUACUCCGAAAGGGAAUCGGGUUAAAAUUCCUGAACCGGGACGUGGCGGUUGACGGCAACGUUAGGAAGUCCGGAGACGUCGGCGGGAGCCUCGGGAAGAGUUAUCUUUUCUGUUUAACAGCCUGCCCACCCUGGAAUCGGCUCAGCCGGAGGUAGGGUCCAGCGGCUGGAAGAGCACCGCACGUCGCGUGGUGUCCGGUGCGCUCCCGGCGGCCCUUGAAAAUCCGGAGGACCGAAUGCCGUCCACGCCCGGUCGUACUCAUAACCGCAUCAGGUCUCCAAGGUGAACAGCCUCUGGUCGAUGGAACAAUGUAGGCAAGGGAAGUCGGCAAAAUGGAUCCGUAACUUCGGGAAAAGGAUUGGCUCUGAGGGCUGGGCACGGGGGUCCCAGUCCCGAACCCGUCGGCUGUCGGUGGACUGCUCGAGCUGCUCCCGCGGCGAGAGCGGGUCGCCGCGUGCCGGCCGGGGGACGGACUGGGAACGGUUCCUUCGGGGGCCUUCCCCGGGCGUCGAACAGCCAACUCAGAACUGGUACGGACAAGGGGAAUCCGACUGUUUAAUUAAAACAAAGCAUUGCGAUGGUCCCAACGGAUGUUUACGCAAUGUGAUUUCUGCCCAGUGCUCUGAAUGUCAAAGUGAAGAAAUUCAACCAAGCGCGGGUAAACGGCGGGAGUAACUAUGACUCUCUUAAGGUAGCCAAAUGCCUCGUCAUCUAAUUAGUGACGCGCAUGAAUGGAUUAACGAGAUUCCCACUGUCCCUGUCUACUAUCCAGCGAAACCACAGCCAAGGGAACGGGCUUGGCAGAAUCAGCGGGGAAAGAAGACCCUGUUGAGCUUGACUCUAGUCCGACUUUGUGAAAUGACUUGAGAGGUGUAGUAUAAGUGGGAGCCGAAAGGCGAAAGUGAAAUACCACUACUUUUAACGUUAUUUUACUUAUUCCGUGAAUCGGAAGCGGGGCACUGCCCCUCUUUUUGGACCCAAGGCUCGCUUCGCGGGCCGAUCCGGGCGGAAGACAUUGUCAGGUGGGGAGUUUGGCUGGGGCGGCACAUCUGUUAAAAGAUAACGCAGGUGUCCUAAGAUGAGCUCAACGAGAACAGAAAUCUCGUGUGGAACAGAAGGGUAAAAGCUCGUUUGAUUCUGAUUUCCAGUACGAAUACGAACCGUGAAAGCGUGGCCUAACGAUCCUUUAGACCUUCGGAAUUCGAAGCUAGAGGUGUCAGAAAAGUUACCACAGGGAUAACUGGCUUGUGGCAGCCAAGCGUUCAUAGCGACGUUGCUUUUUGAUCCUUCGAUGUCGGCUCUUCCUAUCAUUGUGAAGCAGAAUUCACCAAGUGUUGGAUUGUUCACCCACCAAUAGGGAACGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUUAGUUUUACCCUACUGAUGACAGUGUCGCAAUAGUAAUUCAACCUAGUACGAGAGGAACCGUUGAUUCACACAAUUGGCCAUCGCGCUUGGUUGAAAAGCCAGUGGCGCGAAGCUACCGUGUGCUGGAUUAUGACUGAACGCCUCUAAGUCAGAAUCCGGGCUAGAAGCGACGCAUGCGCCCGCCGUCCGCUUGCCGACCCGCAGUAGGGGCCUUUGGCCCCCAAGGGCACGUGUCGUUGGCUAAGUCGCCGCGACGGAAGCGUCGCGGUGACCGCCUUGAAGUACAAUUUCCAUCGAGCGGCGGGUAGAAUCCUUUGCAGACGACUUAAAUACGCGACGGGGUAUUGUAAGUGGCAGAGUGGCCUUGCUGCCACGAUCCACUGAGAUUCAGCCCUUUGUCGCUCCGAUUCGU
5S rRNA 5 120 NA GGAUGCGAUCAUACCAGCACUAACGCACCGGAUCCCAUCAGAACUCCGAAGUUAAGCGUGCUUGGGCGAGAGUAGUACUAGGAUGGGUGACCCCCUGGGAAGUCCUCGUGUUGCAUCCCU
5.8S rRNA 8 165 NA ACAAACGACUCUCGGCAACGGAUAUCUCGGCUCUCGCAUCGAUGAAGAACGUAGCGAAAUGCGAUACUUGGUGUGAAUUGCAGAAUCCCGUGAACCAUCGAGUCUUUGAACGCAAGUUGCGCCCGAAGCCAUUUGGCCGAGGGCACGUCUGCCUGGGCGUCACGC
Experimental Data

Method: ELECTRON MICROSCOPY

Deposited Date: 2021-12-16
Deposition Author(s): Amunts, A. , Cottilli, P. , Itoh, Y.