7QIX
Specific features and methylation sites of a plant ribosome. 40s body ribosomal subunit.
PDB DOI: 10.2210/pdb7qix/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: 2.53 Å
Specific features and methylation sites of a plant ribosome. 40s body ribosomal subunit.
Amunts, A. , Cottilli, P. , Itoh, Y.
Primary Citation of Related Structures: 7QIX
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 18S rRNA body | 2 | 1807 | NA | UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGUAAGUAUGAACAAAUUCAGACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUGUUUGAUGGUAUCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAACCCCGACUUCUGGAAGGGAUGCAUUUAUUAGAUAAAAGGUCGACGCGGGCUCUGCCCGUUGCUGCGAUGAUUCAUGAUAACUCGACGGAUCGCACGGCCAUCGUGCCGGCGACGCAUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUGGUGACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAUAACAAUACCGGGCUCUAUGAGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAXXAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGACUUUGGGAUGGGCCGGCCGGUCCGCCCUAGGUGUGCACCGGUCGUCUCGUCCCUUCUGUCGGCGAUGCGCUCCUGGCCUUAAUUGGCCGGGUCGUGCCUCCGGCGCUGUUACUUUGAAGAAAUUAGAGUGCUCAAAGCAAGCCUACGCUCUGUAUACAUUAGCAUGGGAUAACAUUAUAGGAUUUCGGUCCUAUUACGUUGGCCUUCGGGAUCGGAGUAAUGAUUAACAGGGACAGUCGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGAUCGGCGGAUGUUGCUUUUAGGACUCCGCCGGCACCUUAUGAGAAAUCAAAGUUUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACCAACACGGGGAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAACUAGCUAUGCGGAGGUAUCCCUUCGCGGCCAGCUUCUUAGAGGGACUACGGCCUUUUAGGCCGCGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGUAUUCAACGAGCUUAUAGCCUUGGCCGACAGGCCCGGGUAAUCUUUGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGAUCCGGUGAAAUGUUCGGAUCGCGGCGACGUGGGCGGUUCGCUGCCCGCGACGUCGCGAGAAGUCCAUUGAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCNGUAGGUGAACCUGCGGAAGGAUCAUUG |
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 40S ribosomal protein S21 | L | 82 | Solanum Lycopersicum | MQNDEGQNMDLYIPRKCSATNRLITSKDHASVQLNVGHLDESGVYTGQFTTYALCGFIRAQGDADSAMDRLWQKKKAEVGQQ |
| 40S body ribosomal protein uS12 | M | 142 | Solanum Lycopersicum | MGKTRGMGAGRKLKSHRRRQRWADKSYKKSHLGNEWKKPFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGRKGHAVGDIPGVRFKVVKVSGVSLLALFKEKKEKPRS |
| 40S ribosomal protein S26 | N | 127 | Solanum Lycopersicum | MTFKRRNGGRNKHGRGHVKFIRCSNCGKCCPKDKAIKRFLVRNIVEQAAVRDVQEACAFELYTLPKLYLKMQYCVSCAIHSKVVRVRSRTDRRVREPPQRFRRPRDDLPKTGQAPRPAGGPPAAPRT |
| S5 DRBM domain-containing protein | O | 280 | Solanum Lycopersicum | MAERGAGDRGGFGRGFGGRGGRGGDRGGRGRGGRRPRRETEEEKWVPVTKLGRLVKDGKIRSLEQIYLHSLPIKEFQIIDTLIGPSLKDEVMKIMPVQKQTRAGQRTRFKAFVVVGDGNGHVGLGVKCSKEVATAIRGGIILAKLSVIPVRRGYWGNKIGKPHTVPCKVTGKCGSVTVRMVPAPRGAGIVAARVPKKVLQFAGIEDVFTSSRGSTKTLGNFVKATFDCLMKTYGFLTPDFWKETRFTKSPFQEYFDILAKPANKVIVYATEEAAPERVEA |
| 40S ribosomal protein S6 | P | 249 | Solanum Lycopersicum | MKFNIANPTTGCQKKLEIDDDQKLRAFFDKRISQEVSGDSLGEEFKGYVFKIMGGCDKQGFPMKQGVLTPGRVRLLLYRGTPCFRGYGRRNGERRRKSVRGCIVSPDLSVLNLVIVKKGENDLPGLTDTEKPRMRGPKRASKIRKLFNLSKEDDVRKYVNTYRRNFTTKTGKNASKAPKIQRLVTPLTLQRKRARIADKKKRIAKAKSEAADYQKLLASRLKEQRERRSESLAKKRSRLSAASKPSIAA |
| 40S body ribosomal protein uS4 | Q | 197 | Solanum Lycopersicum | MVHVSFYRNYGKTFKKPRRPYEKERLDAELKLVGEYGLRCKRELWRVQYALSRIRNAARMLLTLDEKDPRRIFEGEALLRRMNRYGLLDESQNKLDYVLALTVENFLERRLQTLVFKTGMAKSIHHARVLIRQRHIRVGRQVVNVASFMVRVDSQKHIDFSLTSPFGGGRPGRVKRKNQKSAAKKAAGGDGDEEDEE |
| 30S ribosomal protein S15, chloroplastic | R | 151 | Solanum Lycopersicum | MGRMHSRGKGISASALPYKRTPPSWLKISAPDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHRLARYYKKTKKLPPVWKYESTTASTLVA |
| Ribosomal protein S14 | S | 150 | Solanum Lycopersicum | MSKRRTREPKEETVTLGPSVREGELVFGVAHIFASFNDTFIHVTDLSGRETMVRITGGMKVKADRDESSPYAAMLAAQDVSQRCKELGINALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPTDSTRRKGGRRGRRL |
| 40S ribosomal protein S24 | U | 133 | Solanum Lycopersicum | MADKAVTIRTRKFMTNRLLARKQFIIDVLHPGRANVSKAELKEKLSRMYEVKDPNAIFVFKFRTHFGGGKSTGFGLIYDSVENAKKYEPKYRLIRNGLDTKVEKSRKQMKERKNRAKKVRGVKKTKAGDAKKK |
| 40S ribosomal protein S27 | V | 86 | Solanum Lycopersicum | MVLPNDVDLLNPPAEHEKKKHKLKRLVQSPNSFFMDVKCQGCFNITTVFSHSQTVVVCGNCQTVLCQPTGGRARLIEGCSFRRKGD |
| 60S ribosomal protein L41 | D | 25 | Solanum Lycopersicum | MRAKWKKKRMRRLKRKRRKMRQRSK |
| 40S ribosomal protein S30 | W | 62 | Solanum Lycopersicum | MGKVHGSLARAGKVRGQTPKVAKQDKKKKPRGRAHKRMQYNRRFVTAVVGFGKKRGPNSSEK |
| 40S ribosomal protein S15a-1 | T | 130 | Solanum Lycopersicum | MVRVSVLNDALKSMYNAEKAGKAQVELRPSSKVIIKFLIVMQKHGYIGDFQYVDDHRVGKIVVELNGRLNKCGVISPRFDVGVATIEGWTARLLPSRQFGYIVLTTSAGIMDHEEARRKNVGGKVLGFFY |
| Ribosomal protein L19 | X | 213 | Solanum Lycopersicum | MVSLKLQKRLAASVLKCGRGKVWLDPNEGNEISMANSRQNIRKLVKDGFIIRKPTKIHSRSRARRMKEAKRKGRHSGYGKRKGTREARLPTKVLWMRRLRVLRRLLRKYRESKKIDKHMYHDMYMKVKGNVFKNKRVLMENIHKTKAEKAREKTLSDQFEARRAKNKASRERKFARRKKRLAQGPGGEKPVQPAAPAAAAPAQPAQGSKKSKK |
| 40S ribosomal protein SA | E | 296 | Solanum Lycopersicum | MATQDVRTLSTKEADIQMMLAAEVHLGTKNCDFQMERYAFKRRNDGIYIINLGKTWEKLQMAARVIVAIENPQDIIVQSARPYGQRAVLKFAQYTGAHAIAGRHTPGTFTNQLQTSYSEPRLLILTDPRTDHQPIKEAALGNIPTIAFCDTDSPMRYVDIGIPANNKGKHSIGVLFWILARMVLQMRGAINQGPKWDVMVDLFFYREPEEAKEQEEEVPAIADYADYSASAALGGDWTSSQIPEAQWTADAAAPAVGGGWAGDGAADGGWDAAAAPAPVPLPVPDVAPTSGATGWE |
| 40S ribosomal protein S3a | F | 260 | Solanum Lycopersicum | MAVGKNKRISKGKKGGKKKAADPYAKKDWYDIKAPSVFEVRNVGKTLVTRTQGTKIASEGLKHRVFEVSLADLQNDEDHSFRKIRLRAEDVQGRNVLTNFHGMDFTTDKLRSLVKKWQSLIEAHVDVKTTDSYTLRMFCIAFTKKRPNQQKRTCYAQSSQIRQIRRKMVEIMRNQAQSCDLKDLVLKFIPESIGREIEKATSSIFPLQNVFIRKVKILKAPKFDLGRLMEVHGDYSEDVGVKVDRPAEDIATEPTEVVGA |
| 40S body ribosomal protein eS4 | G | 264 | Solanum Lycopersicum | MARGLKKHLKRLNAPKHWMLDKLGGAFAPKPSSGPHKSRECLPLVIILRNRLKYALTYREVISILMQRQVMVDGKVRTDKTYPAGFMDVVTIPKTNESFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYLNTYDGRTIRYPDPLIKANDTIKLDLDSNKIVDFIKFDVGNVVMVTGGRNRGRVGILKNREKHKGSFETVHIQDSQGHEFATRLGNVFTLGKGSKPWVSLPKGKGIKLSIIEEARKRMAAQSATPA |
| 40S ribosomal protein S7 | H | 191 | Solanum Lycopersicum | MYTSKQKIHKDKAAEPSEHEVSVGQAFFDLENTNQELKSELKDLYINSATQIDVSGNRKAVVIHVPYRLRKAFRKVHVRLVRELEKKFSGKDVIFIATRRIVRPPKRGSAAQRPRTRTLTSVHDAILEDLVVPAEIVGKRTRYRVDGSKIMKVYLDPKERNNTEYKLETFSAVYRKLSGKDVVFEYPITEA |
| 40S ribosomal protein S8 | I | 220 | Solanum Lycopersicum | MGISRDSMHKRRATGGKKKSWRKKRKYELGRQPANTKISSNKTVRRIRVRGGNVKWRALRLDTGNFSWGSEAVTRKTRILDVVYNASNNELVRTQTLVKSAIVQVDAAPFKQWYLQHYGIDIGRKKKGAAKKETTTEEGDAAEEAKKSNHVVRKIENRQADRKLDSHLEEQFASGRLLACISSRPGQCGRADGYILEGKELEFYMKKLQKKKGKASGASA |
| Ribosomal_S17_N domain-containing protein | J | 159 | Solanum Lycopersicum | MAEQTEKAFLKQPGVFLSSKKTGKGKRPGKGGNRYFKSIGLGFKTPREATEGTYIDKKCPFTGNVSIRGRILAGTCHSAKMNRTIIVRRNYLHYVKKYQRYEKRHSNIPAHISPCFRVKEGDHVTIGQCRPLSKTVRFNVLKVIPAGSGGVGKKAFTGM |
| 40S ribosomal protein S17 | K | 144 | Solanum Lycopersicum | MGRVRTKTVKKSSRQVIERYYSKMTLDFHTNKKILEEVAIIPSKRLRNKIAGFSTHLMKRIQKGPVRGISLKLQEEERERRMDFVPEESAIKTDLIEVDKETLDMLSALGMSDLPGVVKQAAEPQAVAALPSYGRGGGGFGRKY |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2021-12-16 Deposition Author(s): Amunts, A. , Cottilli, P. , Itoh, Y.