7O5B
Cryo-em structure of a bacillus subtilis mifm-stalled ribosome-nascent chain complex with (p)ppgpp-srp bound
PDB DOI: 10.2210/pdb7o5b/pdb
Classification: RIBOSOME Organism(s): Bacillus Subtilis Subsp. Subtilis Str. 168 , Synthetic Construct
Deposited: 2021-04-08 Deposition Author(s): Bange, G. , Beckmann, R. , Berninghausen, O. , Czech, L. , Kratzat, H.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 3.33 Å
Cryo-em structure of a bacillus subtilis mifm-stalled ribosome-nascent chain complex with (p)ppgpp-srp bound
Bange, G. , Beckmann, R. , Berninghausen, O. , Czech, L. , Kratzat, H.
Primary Citation of Related Structures: 7O5B
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 50S ribosomal protein L27 | U | 94 | Bacillus Subtilis Subsp. Subtilis Str. 168 , Synthetic Construct | MLRLDLQFFASKKGVGSTKNGRDSEAKRLGAKRADGQFVTGGSILYRQRGTKIYPGENVGRGGDDTLFAKIDGTVKFERFGRDRKKVSVYPVAQ |
| 50S ribosomal protein L2 | Z | 277 | Bacillus Subtilis Subsp. Subtilis Str. 168 , Synthetic Construct | MAIKKYKPTSNGRRGMTTSDFAEITTDKPEKSLLAPLHKKGGRNNQGKLTVRHQGGGHKRQYRVIDFKRDKDGIPGRVATVEYDPNRSANIALINYADGEKRYILAPKGIQVGTEIMSGPEADIKVGNALPLINIPVGTVVHNIELKPGKGGQLVRSAGTSAQVLGKEGKYVLVRLNSGEVRMILSACRASIGQVGNEQHELINIGKAGRSRWKGIRPTVRGSVMNPNDHPHGGGEGRAPIGRKSPMSPWGKPTLGFKTRKKKNKSDKFIVRRRKNK |
| 30S ribosomal protein S2 | B | 246 | Bacillus Subtilis Subsp. Subtilis Str. 168 , Synthetic Construct | MSVISMKQLLEAGVHFGHQTRRWNPKMKRYIFTERNGIYIIDLQKTVKKVEEAYNFTKNLAAEGGKILFVGTKKQAQDSVKEEAQRSGMYYVNQRWLGGTLTNFETIQKRIKRLKDIEKMQENGTFDVLPKKEVVQLKKELERLEKFLGGIKDMKDLPDALFIIDPRKERIAVAEARKLNIPIIGIVDTNCDPDEIDVVIPANDDAIRAVKLLTSKMADAILEAKQGEEEAEVAEETAPETETTTA |
| 30S ribosomal protein S3 | C | 218 | Bacillus Subtilis Subsp. Subtilis Str. 168 , Synthetic Construct | MGQKVNPVGLRIGVIRDWESKWYAGKDYADFLHEDLKIREYISKRLSDASVSKVEIERAANRVNITIHTAKPGMVIGKGGSEVEALRKALNSLTGKRVHINILEIKRADLDAQLVADNIARQLENRVSFRRAQKQQIQRTMRAGAQGVKTMVSGRLGGADIARSEYYSEGTVPLHTLRADIDYATSEADTTYGKLGVKVWIYRGEVLPTKKKTEEGGK |
| 30S ribosomal protein S4 | D | 200 | Bacillus Subtilis Subsp. Subtilis Str. 168 , Synthetic Construct | MARYTGPSWKLSRRLGISLSGTGKELEKRPYAPGPHGPGQRKKLSEYGLQLQEKQKLRHMYGVNERQFRTLFDKAGKLAGKHGENFMILLDSRLDNVVYKLGLARTRRQARQLVNHGHILVDGSRVDIPSYLVKPGQTIGVREKSRNLSIIKESVEVNNFVPEYLTFDAEKLEGTFTRLPERSELAPEINEALIVEFYSR |
| 30S ribosomal protein S5 | E | 166 | Bacillus Subtilis Subsp. Subtilis Str. 168 , Synthetic Construct | MRRIDPSKLELEERLVTVNRVAKVVKGGRRFRFAALVVVGDKNGHVGFGTGKAQEVPEAIRKAVEDAKKNLIEVPMVGTTIPHEIIGRFGAGNILLKPASEGTGVIAGGPVRAVLELAGVADILSKSLGSNTPINMIRATLQGLSELKRAEDVAKLRGKSVEELLG |
| 30S ribosomal protein S6 | F | 95 | Bacillus Subtilis Subsp. Subtilis Str. 168 , Synthetic Construct | MRKYEVMYIIRPNIDEESKKAVIERFNNVLTSNGAEITGTKDWGKRRLAYEINDFRDGFYQIVNVQSDAAAVQEFDRLAKISDDIIRHIVVKEEE |
| 30S ribosomal protein S9 | I | 130 | Bacillus Subtilis Subsp. Subtilis Str. 168 , Synthetic Construct | MAQVQYYGTGRRKSSVARVRLVPGEGRIVVNNREISEHIPSAALIEDIKQPLTLTETAGTYDVLVNVHGGGLSGQAGAIRHGIARALLEADPEYRTTLKRAGLLTRDARMKERKKYGLKGARRAPQFSKR |
| 30S ribosomal protein S10 | J | 102 | Bacillus Subtilis Subsp. Subtilis Str. 168 , Synthetic Construct | MAKQKIRIRLKAYDHRILDQSAEKIVETAKRSGASVSGPIPLPTEKSVYTILRAVHKYKDSREQFEMRTHKRLIDIVNPTPQTVDALMRLDLPSGVDIEIKL |
| 30S ribosomal protein S11 | K | 131 | Bacillus Subtilis Subsp. Subtilis Str. 168 , Synthetic Construct | MAAARKQNTRKRRVKKNIESGIAHIRSTFNNTIVTITDTHGNAISWSSAGALGFRGSRKSTPFAAQMAAETAAKGSIEHGLKTLEVTVKGPGSGREAAIRALQAAGLEVTAIRDVTPVPHNGCRPPKRRRV |
| 50S ribosomal protein L28 | V | 62 | Bacillus Subtilis Subsp. Subtilis Str. 168 , Synthetic Construct | MARKCVITGKKTTAGNNRSHAMNASKRTWGANLQKVRILVNGKPKKVYVSARALKSGKVERV |
| 30S ribosomal protein S12 | L | 138 | Bacillus Subtilis Subsp. Subtilis Str. 168 , Synthetic Construct | MPTINQLIRKGRVSKVENSKSPALNKGYNSFKKEHTNVSSPQKRGVCTRVGTMTPKKPNSALRKYARVRLTNGIEVTAYIPGIGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGALDTAGVENRAQGRSKYGTKKPKAK |
| 30S ribosomal protein S13 | M | 121 | Bacillus Subtilis Subsp. Subtilis Str. 168 , Synthetic Construct | MARIAGVDIPRDKRVVISLTYIFGIGRTTAQQVLKEAGVSEDTRVRDLTEEELGKIRDIIDKLKVEGDLRREVSLNIKRLIEIGSYRGIRHRRGLPVRGQNSKNNARTRKGPRRTVANKKK |
| 30S ribosomal protein S14 | N | 61 | Bacillus Subtilis Subsp. Subtilis Str. 168 , Synthetic Construct | MAKKSMIAKQQRTPKFKVQEYTRCERCGRPHSVIRKFKLCRICFRELAYKGQIPGVKKASW |
| 30S ribosomal protein S15 | O | 89 | Bacillus Subtilis Subsp. Subtilis Str. 168 , Synthetic Construct | MAITQERKNQLINEFKTHESDTGSPEVQIAILTDSINNLNEHLRTHKKDHHSRRGLLKMVGKRRNLLTYLRNKDVTRYRELINKLGLRR |
| 30S ribosomal protein S18 | R | 79 | Bacillus Subtilis Subsp. Subtilis Str. 168 , Synthetic Construct | MAGGRRGGRAKRRKVCYFTSNGITHIDYKDVDLLKKFVSERGKILPRRVTGTNAKYQRKLTAAIKRARQMALLPYVSGE |
| 30S ribosomal protein S19 | S | 92 | Bacillus Subtilis Subsp. Subtilis Str. 168 , Synthetic Construct | MARSLKKGPFVDGHLMTKIEKLNETDKKQVVKTWSRRSTIFPQFIGHTIAVYDGRKHVPVFISEDMVGHKLGEFAPTRTYKGHASDDKKTRR |
| 30S ribosomal protein S20 | T | 88 | Bacillus Subtilis Subsp. Subtilis Str. 168 , Synthetic Construct | MPNIKSAIKRTKTNNERRVHNATIKSAMRTAIKQVEASVANNEADKAKTALTEAAKRIDKAVKTGLVHKNTAARYKSRLAKKVNGLSA |
| 50S ribosomal protein L32 | 0 | 59 | Bacillus Subtilis Subsp. Subtilis Str. 168 , Synthetic Construct | MAVPFRRTSKMKKRLRRTHFKLNVPGMTECPSCGEMKLSHRVCKACGSYNGKDINVKSN |
| 50S ribosomal protein L33 1 | 1 | 49 | Bacillus Subtilis Subsp. Subtilis Str. 168 , Synthetic Construct | MRVNITLACTECGERNYISKKNKRNNPDRVEFKKYCPRDKKSTLHRETK |
| 50S ribosomal protein L34 | 2 | 44 | Bacillus Subtilis Subsp. Subtilis Str. 168 , Synthetic Construct | MKRTFQPNNRKRSKVHGFRSRMSSKNGRLVLARRRRKGRKVLSA |
| 50S ribosomal protein L35 | 3 | 66 | Bacillus Subtilis Subsp. Subtilis Str. 168 , Synthetic Construct | MPKMKTHRGSAKRFKKTGSGKLKRSHAYTSHLFANKSQKQKRKLRKSAVVSAGDFKRIKQMLANIK |
| 50S ribosomal protein L36 | 4 | 37 | Bacillus Subtilis Subsp. Subtilis Str. 168 , Synthetic Construct | MKVRPSVKPICEKCKVIRRKGKVMVICENPKHKQKQG |
| 50S ribosomal protein L31 | 6 | 66 | Bacillus Subtilis Subsp. Subtilis Str. 168 , Synthetic Construct | MKAGIHPNFKKATVKCACGNEFETGSVKEEVRVEICSECHPFYTGRQKFASADGRVDRFNKKYGLK |
| 30S ribosomal protein S7 | G | 156 | Bacillus Subtilis Subsp. Subtilis Str. 168 , Synthetic Construct | MPRKGPVAKRDVLPDPIYNSKLVSRLINKMMIDGKKGKSQTILYKSFDIIKERTGNDAMEVFEQALKNIMPVLEVKARRVGGANYQVPVEVRPERRTTLGLRWLVNYARLRGEKTMEERLANEILDAANNTGAAVKKREDTHKMAEANKAFAHYRW |
| MifM-stalling construct | H | 96 | Bacillus Subtilis Subsp. Subtilis Str. 168 , Synthetic Construct | GPGTMFVESINDVLFLVDFFTIILPALTAIGIAFLLRECRAGEQWKSKRTDGPGKPIPNPLLGLDSTDFLIIIYHRITTWIRKVFRMNSPVNDEED |
| 50S ribosomal protein L10 | P | 166 | Bacillus Subtilis Subsp. Subtilis Str. 168 , Synthetic Construct | MSSAIETKKVVVEEIASKLKESKSTIIVDYRGLNVSEVTELRKQLREANVEFKVYKNTMTRRAVEQAELNGLNDFLTGPNAIAFSTEDVVAPAKVLNDFAKNHEALEIKAGVIEGKVSTVEEVKALAELPSREGLLSMLLSVLQAPVRNLALATKAVAEQKEEQGA |
| 50S ribosomal protein L11 | Q | 141 | Bacillus Subtilis Subsp. Subtilis Str. 168 , Synthetic Construct | MAKKVVKVVKLQIPAGKANPAPPVGPALGQAGVNIMGFCKEFNARTADQAGLIIPVEISVYEDRSFTFITKTPPAAVLLKKAAGIESGSGEPNRNKVATVKRDKVREIAETKMPDLNAADVEAAMRMVEGTARSMGIVIED |
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 16S rRNA (1533-MER) | a | 1533 | NA | GGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCCUAAUACAUGCAAGUCGAGCGGACAGAUGGGAGCUUGCUCCCUGAUGUUAGCGGCGGACGGGUGAGUAACACGUGGGUAACCUGCCUGUAAGACUGGGAUAACUCCGGGAAACCGGGGCUAAUACCGGAUGGUUGUUUGAACCGCAUGGUUCAAACAUAAAAGGUGGCUUCGGCUACCACUUACAGAUGGACCCGCGGCGCAUUAGCUAGUUGGUGAGGUAACGGCUCACCAAGGCGACGAUGCGUAGCCGACCUGAGAGGGUGAUCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUAGGGAAUCUUCCGCAAUGGACGAAAGUCUGACGGAGCAACGCCGCGUGAGUGAUGAAGGUUUUCGGAUCGUAAAGCUCUGUUGUUAGGGAAGAACAAGUGCCGUUCGAAUAGGGCGGUACCUUGACGGUACCUAACCAGAAAGCCACGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGUGGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGGGCUCGCAGGCGGUUUCUUAAGUCUGAUGUGAAAGCCCCCGGCUCAACCGGGGAGGGUCAUUGGAAACUGGGGAACUUGAGUGCAGAAGAGGAGAGUGGAAUUCCACGUGUAGCGGUGAAAUGCGUAGAGAUGUGGAGGAACACCAGUGGCGAAGGCGACUCUCUGGUCUGUAACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAGUGCUAAGUGUUAGGGGGUUUCCGCCCCUUAGUGCUGCAGCUAACGCAUUAAGCACUCCGCCUGGGGAGUACGGUCGCAAGACUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAGGUCUUGACAUCCUCUGACAAUCCUAGAGAUAGGACGUCCCCUUCGGGGGCAGAGUGACAGGUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGAUCUUAGUUGCCAGCAUUCAGUUGGGCACUCUAAGGUGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAAUCAUCAUGCCCCUUAUGACCUGGGCUACACACGUGCUACAAUGGACAGAACAAAGGGCAGCGAAACCGCGAGGUUAAGCCAAUCCCACAAAUCUGUUCUCAGUUCGGAUCGCAGUCUGCAACUCGACUGCGUGAAGCUGGAAUCGCUAGUAAUCGCGGAUCAGCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCACGAGAGUUUGUAACACCCGAAGUCGGUGAGGUAACCUUUUAGGAGCCAGCCGCCGAAGGUGGGACAGAUGAUUGGGGUGAAGUCGUAACAAGGUAGCCGUAUCGGAAGGUGCGGCUGG |
| SRP RNA (266-MER) | w | 266 | NA | GCCGUGCUAAGCGGGGAGGUAGCGGUGCCCUGUACCUGCAAUCCGCUCUAGCAGGGCCGAAUCCCUUCUCGAGGUUCGUUUACUUUAAGGCCUGCCUUAAGUAAGUGGUGUUGACGUUUGGGUCCUGCGCAAUGGGAAUUCAUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGUGAAACCUCUCAUGUGCCGCAGGGUUGCCUGGGCCGAGCUAACUGCUUAAGUAACGCUAGGGUAGCGAAUCGACAGAAGGUGCACGGU |
| 23S rRNA (2887-MER) | x | 2887 | NA | GUUAAGUUAGAAAGGGCGCACGGUGGAUGCCUUGGCACUAGGAGCCGAUGAAGGACGGGACGAACACCGAUAUGCUUCGGGGAGCUGUAAGCAAGCUUUGAUCCGGAGAUUUCCGAAUGGGGAAACCCACCACUCGUAAUGGAGUGGUAUCCAUAUCUGAAUUCAUAGGAUAUGAGAAGGCAGACCCGGGGAACUGAAACAUCUAAGUACCCGGAGGAAGAGAAAGCAAAUGCGAUUCCCUGAGUAGCGGCGAGCGAAACGGGAUCAGCCCAAACCAAGAGGCUUGCCUCUUGGGGUUGUAGGACACUCGAACGAGGUAGAUGAAGAGGUCUGGAAAGGCCCGCCAUAGGAGGUAACAGCCCUGUAGUCAAAACUUCGUUCGAGUGGAUCCUGAGUACGGCGGAACACGUGAAAUUCCGUCGGAAUCCGGGAGGACCAUCUCCCAAGGCUAAAUACUCCCUAGUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGUGAAAAGCACCCCGGAAGGGGAGUGAAAGAGAUCCUGAAACCGUGUGCCUACAAGUAGUCAGAGCCCGUUAACGGGUGAUGGCGUGCCUUUUGUAGAAUGAACCGGCGAGUUACGAUCUCGUGCAAGGUUAAGCAGAAGAUGCGGAGCCGCAGCGAAAGCGAGUCUGAAUAGGGCGCAUGAGUACGUGGUCGUAGACCCGAAACCAGGUGAUCUACCCAUGUCCAGGGUGAAGUUCAGGUAACACUGAAUGGAGGCCCGAACCCACGCACGUUGAAAAGUGCGGGGAUGAGGUGUGGGUAGGGGUGAAAUGCCAAUCGAACCUGGAGAUAGCUGGUUCUCUCCGAAAUAGCUUUAGGGCUAGCCUCAAGGUAAGAGUCUUGGAGGUAGAGCACUGAUUGGACUAGGGGCCCCUACCGGGUUACCGAAUUCAGUCAAACUCCGAAUGCCAAUGACUUAUCCUUGGGAGUCAGACUGCGAGUGAUAAGAUCCGUAGUCGAAAGGGAAACAGCCCAGACCGCCAGCUAAGGUCCCAAAGUAUACGUUAAGUGGAAAAGGAUGUGGAGUUGCUUAGACAACCAGGAUGUUGGCUUAGAAGCAGCCACCAUUUAAAGAGUGCGUAAUAGCUCACUGGUCGAGUGACUCUGCGCCGAAAAUGUACCGGGGCUAAACGUAUCACCGAAGCUGCGGACUGUUCGAACAGUGGUAGGAGAGCGUUCUAAGGGCUGUGAAGCCAGACCGGAAGGACUGGUGGAGCGCUUAGAAGUGAGAAUGCCGGUAUGAGUAGCGAAAGAGGGGUGAGAAUCCCCUCCACCGAAUGCCUAAGGUUUCCUGAGGAAGGCUCGUCCGCUCAGGGUUAGUCGGGACCUAAGCCGAGGCCGAAAGGCGUAGGCGAUGGACAACAGGUUGAUAUUCCUGUACCACCUCCUCACCAUUUGAGCAAUGGGGGGACGCAGGAGGAUAGGGUAAGCGCGGUAUUGGAUAUCCGCGUCCAAGCAGUUAGGCUGGGAAAUAGGCAAAUCCGUUUCCCAAAGGCUGAGCUGUGAUGGCGAGCGCGAAGUUCCUGAUUCCACACUGCCAAGAAAAGCCUCUAGCGAGGUGAGAGGUGCCCGUACCGCAAACCGACACAGGUAGGCGAGGAGAGAAUCCUAAGGUGAUCGAGAGAACUCUCGUUAAGGAACUCGGCAAAAUGACCCCGUAACUUCGGGAGAAGGGGUGCUCUGUUAGGGUGCAAGCCCGAGAGAGCCGCAGUGAAUAGGCCCAGGCGACUGUUUAGCAAAAACACAGGUCUCUGCGAAGCCGUAAGGCGAAGUAUAGGGGCUGACGCCUGCCCGGUGCUGGAAGGUUAAGAGGAGCGCUUAGCGUAAGCGAAGGUGCGAAUUGAAGCCCCAGUAAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCCGCACGAAAGGCGCAACGAUCUGGGCACUGUCUCAACGAGAGACUCGGUGAAAUUAUAGUACCUGUGAAGAUGCAGGUUACCCGCGACAGGACGGAAAGACCCCGUGGAGCUUUACUGCAGCCUGAUAUUGAAUGUUGGUACAGCUUGUACAGGAUAGGUAGGAGCCUUGGAAACCGGAGCGCCAGCUUCGGUGGAGGCAUCGGUGGGAUACUACCCUGGCUGUAUUGACCUUCUAACCCGCCGCCCUUAUCGGGCGGGGAGACAGUGUCAGGUGGGCAGUUUGACUGGGGCGGUCGCCUCCUAAAAGGUAACGGAGGCGCCCAAAGGUUCCCUCAGAAUGGUUGGAAAUCAUUCGCAGAGUGUAAAGGCACAAGGGAGCUUGACUGCGAGACCUACAAGUCGAGCAGGGACGAAAGUCGGGCUUAGUGAUCCGGUGGUUCCGCAUGGAAGGGCCAUCGCUCAACGGAUAAAAGCUACCCCGGGGAUAACAGGCUUAUCUCCCCCAAGAGUCCACAUCGACGGGGAGGUUUGGCACCUCGAUGUCGGCUCAUCGCAUCCUGGGGCUGUAGUCGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGUACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCCCUAUCCGUCGCGGGCGCAGGAAAUUUGAGAGGAGCUGUCCUUAGUACGAGAGGACCGGGAUGGACGCACCGCUGGUGUACCAGUUGUUCUGCCAAGGGCAUCGCUGGGUAGCUAUGUGCGGACGGGAUAAGUGCUGAAAGCAUCUAAGCAUGAAGCCCCCCUCAAGAUGAGAUUUCCCAUUCCGCAAGGAAGUAAGAUCCCUGAAAGAUGAUCAGGUUGAUAGGUCUGAGGUGGAAGUGUGGCGACACAUGGAGCUGACAGAUACUAAUCGAUCGAGGACUUAACC |
| 5S rRNA (112-MER) | y | 112 | NA | UGGUGGCGAUAGCGAAGAGGUCACACCCGUUCCCAUACCGAACACGGAAGUUAAGCUCUUCAGCGCCGAUGGUAGUCGGGGGUUUCCCCCUGUGAGAGUAGGACGCCGCCAA |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2021-04-08 Deposition Author(s): Bange, G. , Beckmann, R. , Berninghausen, O. , Czech, L. , Kratzat, H.