5MLC
Cryo-em structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions
PDB DOI: 10.2210/pdb5mlc/pdb
Classification: RIBOSOME Organism(s): Eubacterium Ramulus
Deposited: 2016-12-06 Deposition Author(s): Arenz, S. , Doenhoefer, A. , Graf, M. , Huter, P. , Novacek, J. , Wilson, D.N.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 3.6 Å
Cryo-em structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions
Arenz, S. , Doenhoefer, A. , Graf, M. , Huter, P. , Novacek, J. , Wilson, D.N.
Primary Citation of Related Structures: 5MLC
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 23S ribosomal RNA, chloroplastic | a | 2811 | NA | UUCAAACGAGGAAAGGCUUACGGUGGAUACCUAGGCACCCAGAGACGAGGAAGGGCGUAUUAAUCGACGAAAUGCUUCGGGGAGUUGAAAAUAAGCAGAGAUCCGGAGAUUCCCGAAUAGGUCAACCUUUCGAACUUCUGCUGAAUCCAUGGGCAGGCAAGAGACAACCUGGCGAACUGAAACAUCUUAGUAGCCAGAGGAAAAGAAAGCAAAAGCGAUUCCCGUAGUAGCGGCGAGCGAAAUGGGAGCAGCCUAAACCGUGAAAACGGGGUUGUGGGAGAGCAAUACAAGCGUCGUGCUGCUAGGCGAAUCAGUGGAGUGCGGAACCCUAGAUGGUGAAAGUCCAGUAGCCGAAAGCAUCACUAGCUUAUGCUCUGACCCGAGUAGCAUGGGGCACGUGGAAUCCCGUGUGAAUCAGCAAGGACCACCUUGCAAGGCUAAAUACUCCUGGGUGACCGAUAGCGAAGUAGUACCGUGAGGGAAGGGUGAAAAGAACCCCCAUCGGGGAGUGAAAUAGAACAUGAAACCGUAAGCUCUCAAGCAGUGGGAGGGGGACCAGACCCUGACCGCGUGCCUGUUGAAGAAUGAGCCGGCGACUCAUAGGCAGUGGCUUGGUUAAGGGAACCCACCGGAGCCGUAGCGAAAGCGAGUCUUCAUAGGGCAAUUGUCACUGCUUAUGGACCCGAACCUGGGUGAUCUAUCCAUGACCAGGAUGAAGCUUGGGUGAAACUAAGUGGAGGUCCGAACCGACUGAUGUUGAAGAAUCAGCGGAUGAGUUGUGGUUAGGGGUGAAAUGCCACUCGAACCCAGAGCUAGCUGGUUCUCCCCGAAAUGCGUUGAGGCGCAGCAGUUGACUGGACAUCUAGGGGUAAAGCACUGUUUCGGUGCGGGCCGCGAGAGCGGUACCAAAUCGAGGCAAACUCUGAAUACUAGAUAUGACCUCCAAAUAACAGGGGUCAAGGUCGGCCAGUGAGACGAUGGGGGAUAAGCUUCAUCGUCGAGAGGGAAACAGCCCGGAUCACCAGCUAAGGCCCCUAAAUGACCGCUCAGUGAUAAAGGAGGUAGGGGUGCAGAGACAGCCAGGAGGUUUGCCUAGAAGCAGCCACCCUUGAAAGAGUGCGUAAUAGCUCACUGAUCGAGCGCUCUUGCGCCGAAGAUGAACGGGGCUAAGCGGUCUGCCGAAGCUGUGGGAUGUAAAAAAACAUCGGUAGGGGAGCGUUCCGUGUUAGGGAGAAACGCGUGCGUGAGCCGCGUUGGACGAAGCGGAAGCGAGAAUGUCGGCUUGAGUAACGCAAACAUUGGUGAGAAUCCAAUGCCCCGAAAACCUAAGGGUUCCUCCGCAAGGUUCGUCCACGGAGGGUGAGUCAGGGCCUAAGAUCAGGCCGAAAGGCGUAGUCGAUGGACAACAGGUGAAUAUUCCUGUACUACCCCUUGUUGGUCCCGAGGGACGGAGGAGGCUAGGUUAGCCGAAAGAUGGUUAUCGGUUCAAGGACGCAAGGUGACCCUGUUUUUCAGGGUAAGAAGGGGUAGAGAAAAUGCCUCGAGCCAAUGUUCGAGUACCAGGCGCUACGGCGCUGAAGUAACCGAUGCCAUACUCCCAGGAAAAGCUCGAACGACCUUCAACAAAAGGGUACCUGUACCCGAAACCGACACAGGUAGGUAGGUAGAGAAUACCUAGGGGCGCGAGACAACUCUCUCUAAGGAACUCGGCAAAAUAGCCCCGUAACUUCGGGAGAAGGGGUGCCCCCUCACAAAGGGGGUCGAAGUGACCAGGCCCGGGCGACUGUUUACCAAAAACACAGGUCUCCGCAAAGUCGUAAGACCAUGUAUGGGGGCUGACGCCUGCCCAGUGCCGGAAGGUCAAGGAAGUUGGUGACCUGAUGACAGGGGAGCCGGCGACCGAAGCCCCGGUGAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCCGCACGAAAGGCGUAACGAUCUGGGCACUGUCUCGGAGAGAGGCUCGGUGAAAUAGACAUGUCUGUGAAGAUGCGGACUACCUGCACCUGGACAGAAAGACCCUAUGAAGCUUUACUGUUCCCUGGGAUUGGCUUUGGGCUUUUCCUGCGCAGCUUAGGUGGAAGGCGAAGAAGGCCCCCUUCCGGGGGGGCCCGAGCCAUCAGUGAGAUACCACUCUGGAAGAGCUAGAAUUCUAACCUUGUGUCAGGACCUACGGGCCAAGGGACAUUCUCAGGUAGACAGUUUCUAUGGGGCGUAGGCCUCCCAAAAGGUAACGGAGGCGUGCAAAGGUUUCCUCGGGCCGGACGGAGAUUGGCCCUCGAGUGCAAAGGCAGAAGGGAGCUUGACUGCAAGACCCACCCGUCGAGCAGGGACGAAAGUCGGCCUUAGUGAUCCGACGGUGCCGAGUGGAAGGGCCGUCGCUCAACGGAUAAAAGUUACUCUAGGGAUAACAGGCUGAUCUUCCCCAAGAGUUCACAUCGACGGGAAGGUUUGGCACCUCGAUGUCGGCUCUUCGCCACCUGGGGCUGUAGUAUGUUCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGUACGUGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCCAUAUCCGGUGUGGGCGUUAGAGCAUUGAGAGGACCUUUCCCUAGUACGAGAGGACCGGGAAGGACGCACCUCUGGUGUACCAGUUAUCGUGCCCACGGUAAACGCUGGGUAGCCAAGUGCGGAGCGGAUAACUGCUGAAAGCAUCUAAGUAGUAAGCCCACCCCAAGAUGAGUGCUCUCCUAU |
| 5S ribosomal RNA, chloroplastic | b | 121 | NA | UAUUCUGGUGUCCUAGGCGUAGAGGAACCACACCAAUCCAUCCCGAACUUGGUGGUUAAACUCUACUGCGGUGACGAUACUGUAGGGGAGGUCCUGCGGAAAAAUAGCUCGACGCCAGGAU |
| 4.8S ribosomal RNA, chloroplastic | c | 103 | NA | GAAGGUCACGGCGAGACGAGCCGUUUAUCAUUACGAUAGGUGUCAAGUGGAAGUGCAGUGAUGUAUGCAGCUGAGGCAUCCUAACAGACCCACAGACUUGAAC |
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 50S ribosomal protein L13, chloroplastic | L | 250 | Eubacterium Ramulus | MATMACASSLTFPSAQTQKSFFGTNVKQTPVLSFPRPTVAAAVAVSARKSTSASTKCTEEWRQLKEAVKKEFAIPHVPLDQRWMFTLEEATGPDIWNTTWYPKSADHVPTDKKWYVVDATDLILGRMASTIAIHIRGKNLASYTPSVDMGAFVIVVNADKVAVSGKKRTQKLYRRHSGRPGGLKEETFDQLQKRIPERIIEHAVRGMLPKGRLGRYLFNHLKVYKGAEHPHQAQQPIDLPLRDKRIRVEK |
| 50S ribosomal protein L14, chloroplastic | M | 121 | Eubacterium Ramulus | MIQPQTHLNVADNSGARELMCIRIIGASNRRYARIGDVIVAVIKEAIPNTPLERSEVIRAVVVRTCKELKRDNGMIIRYDDNAAVIIDQEGNPKGTRIFGAIARELRQKFAKIVSLAPEVL |
| 50S ribosomal protein L15, chloroplastic | N | 271 | Eubacterium Ramulus | MASLLSLSSTPPSTANSNNYPSSTFKGNINNFRINPFNFAPLKLHLRNIVKKESTRLVVVASASSSNVSPSIGSGSETRFRLDNLGPQPGSRKKGKRKGRGHAAGQGGSCGFGMRGQKSRSGPGIMRGFEGGQMPLYRRIPKLRGIAGGMRAGLPKYVPINLRDIEVAGFKEGEEVSLESLKAKGIINPSGRERRLPLKILGEGELSTKLQIKARAFSGSAKEKLEAAGCSVTVLPGRKKYIKESVRKNLARADEYFAKKRAASASEAESA |
| 50S ribosomal protein L16, chloroplastic | O | 135 | Eubacterium Ramulus | MLSPKRTRFRKQHRGRMKGISYRGNRICFGRYALQALEPAWITSRQIEAGRRAMTRNARRGGKIWVRIFPDKPVTVRPAETRMGSGKGSPEYWVAVVKPGRILYEISGVAENIARRAVAIAASKMPIRTQFIISG |
| 50S ribosomal protein L17, chloroplastic | P | 126 | Eubacterium Ramulus | MIDNGGRFFAMKHGRKIHRLSRPADQRRALLRGLTTQLLKHGRIKTTRAKASAMRKYVDKMITLAKEGSLHKRRQALGFIYEKQIVHALFAEVPERYGDRNGGYTRIIRTLPRRGDNAPMAYIELV |
| 50S ribosomal protein L18, chloroplastic | Q | 166 | Eubacterium Ramulus | MAAATSLSFFHSTLASSSSSSVQQLSLPPKFVNFRPQTLPLIQAKAHTRREDRTARHVRIRKKVEGTPERPRLCVFRSNKHLYVQVIDDTKMHTLAAASTMQKAISENIDYSAGPTVEVAQKIGEMIAKSCLEKGITKVAFDRGGYPYHGRVKALADAAREHGLVF |
| 50S ribosomal protein L19, chloroplastic | R | 233 | Eubacterium Ramulus | MASKVLPQALLVIPSNHSLQCPPLKKQLGFPIDSNRRFSLSSNCRSNLMVSRASSNLFSSNFSSIFSFPARNSFVVRSEAEDSSDAPAESVAVVAEEELPVESEAEAEERPPRQQRVKLGDIMGILNKKAVHAAEELRPVPGIRTGDIVQIRLEVPENKRRLSVYKGIVISRQNAGIHTTIRIRRIIAGVGVEIVFPLYSPNIKEIKVVSHRKVRKARLYYLRDKLPRLSTFK |
| 50S ribosomal protein L20, chloroplastic | S | 128 | Eubacterium Ramulus | MTRVKRGYIARRRRKKIRFFASSFRGAHSRLTRTIAQQKIRALVSAHRDRDRQKRDFRRLWITRINAAIRERGVYYNYSKFIHDLYKRQLLLNRKILAQIAILNPNCIYMIYNEIIKKEDCKKYLEII |
| 50S ribosomal protein L21, chloroplastic | T | 256 | Eubacterium Ramulus | MASATLAFSCSSLCATLKLPQNLNPLLLNVPPLSKPFSGVVSPPSLSRLSLLPVAAKRRRFQEIPEELKAEFEEFQRPPNQKPQLSDVLPDDFQAPEPGTPEYNDIINQFLPKKGPPPPREEIFAVVVIGSRQYIVIPGRWIYTQRLKGATVNDKIVLNKVLLVGTKASTYIGTPIVTNAAVHAVVEEQLLDDKVIVFKYKKKKNYRRNIGHRQPITRIKITGITGYEDYPASTLEAEVEAKEEAEAEAEAEAVPV |
| 50S ribosomal protein L22, chloroplastic | U | 199 | Eubacterium Ramulus | MGFFKKKEKKAEFDVFRLYGLHHPEPGKCDEITTRGYSISMSVDKARRVIDQIRGRSYAETLMILELMPYRACYPIFKLIYSAAANASHNKQFNKANLIISKAEVNKGITLKKVKPRARGRSYMIKRPTCHITIVLRDITHFDSYDKFLESLTPKKLIALLGLMSTGRRRELLCGRFRENHKIKSFLYKIALFKRYEVM |
| 50S ribosomal protein L23, chloroplastic | V | 198 | Eubacterium Ramulus | MATTAPNLHSLSSSFAFSNPSSNVSATSFTFQIPNKKAQISCISSKKLHTQKSFNFHDAVTPMNKPSFGRDLMVAQATEAVAPTTEEAATSQPKTSKKAKKLKYPRRILDVYQILQSPIITEAAIKNIADENSLLFTVDVRADKKMIREAISNFFGVKVRKVNTLIRPDGTKKAYIMLNKEYNASELAKKIGIFPGGN |
| 50S ribosomal protein L24, chloroplastic | W | 191 | Eubacterium Ramulus | MAAMVLQSSFTSLSLSSNSFLGQRLFPSPTTLQVKTEGHSPCLIVMRIKRWERKDCKPNSLPKLHKRHVKVGDTVKVISGGEKGKIGEISKIHKHNSTVIIKDLNFKTKHVKSKEEGEQGQIIKIEAAIHSSNVMLILKEQEVADRVGHKILEDVRKVRYLIKTGEIVDTPDRWKEIQNKKESETAVAVAA |
| 50S ribosomal protein L27, chloroplastic | X | 194 | Eubacterium Ramulus | MAVTTSMSFNLMASFRGMSLSSSSSSSFFKGEFGPSSLRLPNKSPLSVSPFPLTIESAHKKGAGSTKNGRDSKGQRLGVKIYGDQVAKPGAIIIRQRGTKFHPGKNVGIGKDHTIFALIDGLVKFEKYGPDKKKVSVYPREIQPENPNSYRARKRENFRLQREKKKARREGYSFQPQLILASAATDNADESAVC |
| 50S ribosomal protein L28, chloroplastic | Y | 148 | Eubacterium Ramulus | MAASGMLISNPSNVCFRKPQFSCSLKPKATVSELGFLTSQLSGIQISPSPLFPIISKPISAPLKPSLQPVARRICPFTGKKSNKANRVSHSNHKTKRLQFVNLQYKRVWWEAGKRFVKLRLSTKALKTIEKNGLDAVAKKAGIDLRKE |
| 50S ribosomal protein L29, chloroplastic | Z | 168 | Eubacterium Ramulus | MLAIHSLSSTPCSSGLTSPPKSTLLTKSSFHGLRLPSVNLSSSLRLRVQTPPSSVVVMVKKEDELKELRTKTNEQLNEEILQLKGELFMLRLQRSARENFKPSDFGRMRKRVARMLTVKREREIEQGVGKRLSRKLDKAWKRSIVVRPPPSLKKLQEKATAEAEAEKA |
| 50S ribosomal protein L32, chloroplastic | 2 | 57 | Eubacterium Ramulus | MAVPKKRTSIYKKRIRKNIWKKKGYWAALKAFSLAKSLSTGNSKSFFVRKISNQTLE |
| 50S ribosomal protein L33, chloroplastic | 3 | 66 | Eubacterium Ramulus | MAKGKDVRVKVILECTGCVRKSVNKGSRGVSRYITQKNRHNTPSRLELRKFCPYCYKHTIHGEIKK |
| 50S ribosomal protein L34, chloroplastic | 4 | 152 | Eubacterium Ramulus | MATLSLLSTGVGAAITNRTPSASLTFITGSRTTNKRVSFNGGSARSGSLHCSFLAPSSSLSSNFSGLSLGLDLTSNTGVSTDRCRRFVVRAGKAALCLTKRSRSRKSLARTHGFRLRMSTTSGRALLKRRRAKGRKILCTKTNPSSGKRASP |
| 50S ribosomal protein L35, chloroplastic | 5 | 159 | Eubacterium Ramulus | MAMASATATLSFKTPSLSLSPPSTRCSAAQGISLTHFNKQLKSTLNLSSSSSISSSKVQPIVLKNKRISTVDSSVSTSSPSFTVFAAKGYKMKTHKASAKRFRVTGKGKIVRRRAGKQHLLAKKNTKRKNRLSKLIQVDRSDYDNVIGALPYLKVNRKV |
| 50S ribosomal protein L36, chloroplastic | 6 | 37 | Eubacterium Ramulus | MKIRASVRPICEKCRLIRRRGRIIVICSNPKHKQRQG |
| Ribosome-recycling factor, chloroplastic | 9 | 271 | Eubacterium Ramulus | MAASSLSSATSYLHSFRRRNSCVSLQGVSDMECNIARTNVSVWRSSANYVRMDCGVKKFSGKAVVVKQLQNRAGTFRCATMEEVEAEKSLIETNTKQRMEKTIETIRSNFNSVRTNRASPTMLDRIEVEYYGTPVSLKSIAQISTPDASSLLISPYDKSSLKAIEKAIVTSQLGVSPNNDGEVIRLSLPPLTSDRRKELAKVVSKLAEEGKVAVRNIRRDALKSYEKLEKEKKLSEDNVKDLSADLQKLTDEYMKKVESIYKQKEQELMKV |
| PSRP5alpha, chloroplastic | 7 | 142 | Eubacterium Ramulus | MALLSPLLSLSSVPPITSIAVSSSSFPIKLQNVSVALLPSFGQRLVAHGPVIAQKRGTVVAMVSAAAEETAGEDGDQSKVEEANISVQNLPLESKLQLKLEQKIKMKMAKKIRLRRTGLCAKESLRKRGAWPPSKMKKLKNV |
| PSRP6, chloroplastic | 8 | 116 | Eubacterium Ramulus | MSVSAIFGARVVTIPSVLRTSSVDGRTVKLQPSTGGSCGGGVITIECSSRPQKKGTAHHMKTRPKKTARWDIKRGPAVYPPLPPLPAEWTIVSSAVDEADSSSSTTSSSAEIAQSA |
| 50S ribosomal protein L2, chloroplastic | D | 272 | Eubacterium Ramulus | MAIHLYKTSTSSTRNGAVQVKSNPRNNLISGQRRCGKGRNARGIITARHRGGGHKRLYRKIDFRRNEKDIYGKIVTIEYDPNRNAYICLIHYGDGEKRYILHPRGAIIGDTIVSGTEVPIKMGNALPLTDMPLGTAIHNIEITLGRGGQLARAAGAVAKLIAKEGKSATLKLPSGEVRLISKNCSATVGQVGNVGVNQKRLGRAGSKRWLGKRPVVRGVVMNPVDHPHGGGEGRAPIGRKSPTTPWGYPALGRRSRKRNKYSDNFIIRRRSK |
| 50S ribosomal protein L3, chloroplastic | E | 305 | Eubacterium Ramulus | MAAILPTFSIKSSSCTYSSSKRSLSSPKAVSLSSSVNGTPKVQSLRLSTSFVCSPNQIIKLKSVSPSRSTQLRRAVGGLEIKMMSVDAGIGVMGTKLGMMSFFEEDGTVVPVTVIGFKEGNIVTQVKTESTDGYNAVQVGYERLRDRKLTMPERGHLNKAGVIPMRHLQEFRLVSVDDFTPSQKLLFEELFKEGDMVDISGTTIGKGFQGGIKRHNFKRGLMTHGSKSHRALGSIGAGTTPGHVYKGKKMPGRMGGTKTKIRKLKIMKIDTDLRVVMIKGAVPGKPGNLLRLAPAKIVGKNIPKN |
| 50S ribosomal protein L4, chloroplastic | F | 293 | Eubacterium Ramulus | MATSTSSSLSLSFFSSSLFSSKSRNFSSKPILKLPSSSHSQTSLSLSIKSELIPLPILNFSGEKVGETFLNLKTAPPEKARAVVHRGLITHLQNKRRGTASTLTRAEVRGGGRKPYPQKKTGRARRGSQGSPLRPGGGVIFGPKPRDWTIKMNKKERRLALSTAIASAVGNSFVVEEFAENFEKPKTKDFIAAMQRWGLDPAEKSLFFLMDLVENVEKSGRNIRTLKLLTPRSLNLFDVLNAEKLVFTEGTIQYLNQRYGVDTLEDEDEEEEEEEEGEEVDDGVEDGTPEPAE |
| 50S ribosomal protein L5, chloroplastic | G | 220 | Eubacterium Ramulus | AAGTAVFVDKAEAETINRLKTNYIEKMVPLLKEEFSYSNILEVPKVVKIVVNCGIGDASQNAKGLDAAINELALITGQRPVKTKAKTSIAGFKVREGMTLGIAVTLRGNLMYSFLDRLINLALPRTRDFQGVNPNSFDGHGNYSVGFREQSVFPEIKPEIVGKARGMDVCITTTAKTDKEAYKLLSLMGMPFREGSGPSTLVRKKKLKSHHFDAKKGRRY |
| 50S ribosomal protein L6, chloroplastic | H | 220 | Eubacterium Ramulus | MSLPLPSHMKSVFLGMKVEISTSVPVTRIGFWRKSVDCKESRIGKQPITVPANVAIAMEGQDLKVKGPLGELSITYPREVLVEKQESGFLRVRKAVETRRANQMHGLFRTLTDNMVVGVSKGFEKKLQLVGVGYRATVEGKDLILSLGFSHPVRMAIPDELQVKVEENTKVTVSGRDKSVVGQFAATIRSWRPPEPYKGKGVRYVDEVVRRKEGKAGKKK |
| 50S ribosomal protein L9, chloroplastic | I | 196 | Eubacterium Ramulus | MASTTSTLSLSWSNSFHSFAGAISEPQKSPENCRVMLPIVAQKKVKKIRKIILKEDIPDLGKKGQLLDVRAGFLRNFLLPLGKAEVVTPLLLKEMKMEDERIEAEKKRVKEEAQQLARMFETVGAFKVKRKGGKGKQIFGSVTAQDLVDIIKAQLQRDVDKKVVFLPDIRETGEYIAELKLHPDVTAQVRVTVFAN |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2016-12-06 Deposition Author(s): Arenz, S. , Doenhoefer, A. , Graf, M. , Huter, P. , Novacek, J. , Wilson, D.N.