5ME1
Structure of the 30s pre-initiation complex 2 (30s ic-2) stalled by ge81112
PDB DOI: 10.2210/pdb5me1/pdb
Classification: RIBOSOME Organism(s): Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Ki Polyomavirus , Haementeria Ghilianii
Deposited: 2016-11-14 Deposition Author(s): Brandi, L. , Connell, S. , Fabbretti, A. , Fucini, P. , Gil Carton, D. , Gualerzi, C. , Iturrioz, I. , Kaminishi, T. , Lopez-Alonso, J.P.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 13.5 Å
Structure of the 30s pre-initiation complex 2 (30s ic-2) stalled by ge81112
Brandi, L. , Connell, S. , Fabbretti, A. , Fucini, P. , Gil Carton, D. , Gualerzi, C. , Iturrioz, I. , Kaminishi, T. , Lopez-Alonso, J.P.
Primary Citation of Related Structures: 5ME1
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 16S ribosomal RNA | a | 1534 | NA | AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUUCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUUGACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCCUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGAAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUAGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCA |
| fMet-tRNA | x | 77 | NA | CGCGGGGUGGAGCAGCCUGGUAGCUCGUCGGGCUCAUAACCCGAAGAUCGUCGGUUCAAAUCCGGCCCCCGCAACCA |
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 30S ribosomal protein S10 | J | 103 | Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Ki Polyomavirus , Haementeria Ghilianii | MQNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKDARDQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISLG |
| 30S ribosomal protein S11 | K | 129 | Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Ki Polyomavirus , Haementeria Ghilianii | MAKAPIRARKRVRKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTPFAAQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHNGCRPPKKRRV |
| 30S ribosomal protein S12 | L | 123 | Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Ki Polyomavirus , Haementeria Ghilianii | ATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNGFEVTSYIGGEGHNLQEHSVILIRGGRVKXLPGVRYHTVRGALDCSGVKDRKQARSKYGVKRPKA |
| 30S ribosomal protein S13 | M | 118 | Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Ki Polyomavirus , Haementeria Ghilianii | MARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVAKFVVEGDLRREISMSIKRLMDLGCYRGLRHRRGLPVRGQRTKTNARTRKGPRKPIKK |
| 30S ribosomal protein S14 | N | 101 | Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Ki Polyomavirus , Haementeria Ghilianii | MAKQSMKAREVKRVALADKYFAKRAELKAIISDVNASDEDRWNAVLKLQTLPRDSSPSRQRNRCRQTGRPHGFLRKFGLSRIKVREAAMRGEIPGLKKASW |
| 30S ribosomal protein S15 | O | 89 | Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Ki Polyomavirus , Haementeria Ghilianii | MSLSTEATAKIVSEFGRDANDTGSTEVQVALLTAQINHLQGHFAEHKKDHHSRRGLLRMVSQRRKLLDYLKRKDVARYTQLIERLGLRR |
| 30S ribosomal protein S16 | P | 102 | Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Ki Polyomavirus , Haementeria Ghilianii | MTPDSVPRWGPVVLFTQEDVMVTIRLARHGAKKRPFYQVVVADSRNARNGRFIERVGFFNPIASEKEEGTRLDLDRIAHWVGQGATISDRVAALIKEVNKAA |
| 30S ribosomal protein S17 | Q | 84 | Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Ki Polyomavirus , Haementeria Ghilianii | MTDKIRTLQGRVVSDKMEKSIVVAIERFVKHPIYGKFIKRTTKLHVHDENNECGIGDVVEIRECRPLSKTKSWTLVRVVEKAVL |
| 30S ribosomal protein S18 | R | 75 | Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Ki Polyomavirus , Haementeria Ghilianii | MARYFRRRKFCRFTAEGVQEIDYKDIATLKNYITESGKIVPSRITGTRAKYQRQLARAIKRARYLSLLPYTDRHQ |
| 30S ribosomal protein S19 | S | 92 | Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Ki Polyomavirus , Haementeria Ghilianii | MPRSLKKGPFIDLHLLKKVEKAVESGDKKPLRTWSRRSTIFPNMIGLTIAVHNGRQHVPVFVTDEMVGHKLGEFAPTRTYRGHAADKKAKKK |
| 30S ribosomal protein S2 | B | 241 | Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Ki Polyomavirus , Haementeria Ghilianii | MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKIASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQSQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLGIPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEAE |
| 30S ribosomal protein S20 | T | 87 | Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Ki Polyomavirus , Haementeria Ghilianii | MANIKSAKKRAIQSEKARKHNASRRSMMRTFIKKVYAAIEAGDKAAAQKAFNEMQPIVDRQAAKGLIHKNKAARHKANLTAQINKLA |
| 30S ribosomal protein S21 | U | 71 | Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Ki Polyomavirus , Haementeria Ghilianii | MPVIKVRENEPFDVALRRFKRSCEKAGVLAEVRRREFYEKPTTERKRAKASAVKRHAKKLARENARRTRLY |
| Translation initiation factor IF-1 | V | 72 | Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Ki Polyomavirus , Haementeria Ghilianii | MAKEKDTIRTEGVVTEALPNATFRVKLDSGPEILAYISGKMRMHYIRILPGDRVVVEITPYDPTRGRIVYRK |
| Translation initiation factor IF-2 | W | 890 | Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Ki Polyomavirus , Haementeria Ghilianii | MTDVTIKTLAAERQTSVERLVQQFADAGIRKSADDSVSAQEKQTLIDHLNQKNSGPDKLTLQRKTRSTLNIPGTGGKSKSVQIEVRKKRTFVKRDPQEAERLAAEEQAQREAEEQARREAEESAKREAQQKAEREAAEQAKREAAEQAKREAAEKDKVSNQQDDMTKNAQAEKARREQEAAELKRKAEEEARRKLEEEARRVAEEARRMAEENKWTDNAEPTEDSSDYHVTTSQHARQAEDESDREVEGGRGRGRNAKAARPKKGNKHAESKADREEARAAVRGGKGGKRKGSSLQQGFQKPAQAVNRDVVIGETITVGELANKMAVKGSQVIKAMMKLGAMATINQVIDQETAQLVAEEMGHKVILRRENELEEAVMSDRDTGAAAEPRAPVVTIMGHVDHGKTSLLDYIRSTKVASGEAGGITQHIGAYHVETENGMITFLDTPGHAAFTSMRARGAQATDIVVLVVAADDGVMPQTIEAIQHAKAAQVPVVVAVNKIDKPEADPDRVKNELSQYGILPEEWGGESQFVHVSAKAGTGIDELLDAILLQAEVLELKAVRKGMASGAVIESFLDKGRGPVATVLVREGTLHKGDIVLCGFEYGRVRAMRNELGQEVLEAGPSIPVEILGLSGVPAAGDEVTVVRDEKKAREVALYRQGKFREVKLARQQKSKLENMFANMTEGEVHEVNIVLKADVQGSVEAISDSLLKLSTDEVKVKIIGSGVGGITETDATLAAASNAILVGFNVRADASARKVIEAESLDLRYYSVIYNLIDEVKAAMSGMLSPELKQQIIGLAEVRDVFKSPKFGAIAGCMVTEGVVKRHNPIRVLRDNVVIYEGELESLRRFKDDVNEVRNGMECGIGVKNYNDVRTGDVIEVFEIIEIQRTIA |
| Translation initiation factor IF-3 | Y | 171 | Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Ki Polyomavirus , Haementeria Ghilianii | SKDFIINEQIRAREVRLIDQNGDQLGIKSKQEALEIAARRNLDLVLVAPNAKPPVCRIMDYGKFRFEQQKKEKEARKKQKVINVKEVRLSPTIEEHDFNTKLRNARKFLEKGDKVKATIRFKGRAITHKEIGQRVLDRLSEACADIAVVETAPKMDGRNMFLVLAPKNDNK |
| Translation initiation factor IF-3 | Z | 144 | Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Ki Polyomavirus , Haementeria Ghilianii | MSLREALEKAEEAGVDLVEISPNAEPPVCRIMDYGKFLYEKSKSSKEQKKKQKVIQVKEIKFRPGTDEGDYQVKLRSLIRFLEEGDKAKITLRFRGREMAHQQIGMEVLNRVKDDLQELAVVESFPTKIEGRQMIMVLAPKKKQ |
| 30S ribosomal protein S3 | C | 233 | Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Ki Polyomavirus , Haementeria Ghilianii | MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERPAKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSITSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRADIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK |
| 30S ribosomal protein S4 | D | 206 | Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Ki Polyomavirus , Haementeria Ghilianii | MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQKVRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEGTFKRKPERSDLSADINEHLIVELYSK |
| 30S ribosomal protein S5 | E | 167 | Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Ki Polyomavirus , Haementeria Ghilianii | MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAIQKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGVHNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK |
| 30S ribosomal protein S6 | F | 131 | Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Ki Polyomavirus , Haementeria Ghilianii | MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYVLMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANETADDAEAGDSEE |
| 30S ribosomal protein S7 | G | 156 | Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Ki Polyomavirus , Haementeria Ghilianii | MPRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELEAFEVALENVRPTVEVKSRRVGGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRLANELSDAAENKGTAVKKREDVHRMAEANKAFAHYRW |
| 30S ribosomal protein S8 | H | 130 | Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Ki Polyomavirus , Haementeria Ghilianii | MSMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELELTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAGLGGEIICYVA |
| 30S ribosomal protein S9 | I | 130 | Sphingobium Sp. (Strain Nbrc 103272 / Syk-6) , Ki Polyomavirus , Haementeria Ghilianii | MAENQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEKLDLYITVKGGGISGQAGAIRHGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRKARRRPQFSKR |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2016-11-14 Deposition Author(s): Brandi, L. , Connell, S. , Fabbretti, A. , Fucini, P. , Gil Carton, D. , Gualerzi, C. , Iturrioz, I. , Kaminishi, T. , Lopez-Alonso, J.P.