5ND9
Hibernating ribosome from staphylococcus aureus (rotated state)
PDB DOI: 10.2210/pdb5nd9/pdb
Classification: RIBOSOME Organism(s): Staphylococcus Aureus (Strain Nctc 8325) , Staphylococcus Aureus Subsp. Aureus Nctc 8325
Deposited: 2017-03-07 Deposition Author(s): Ayupov, R. , Hashem, Y. , Khusainov, I. , Kieffer, B. , Myasnikov, A. , Simonetti, A. , Usachev, K. , Validov, S. , Vicens, Q. , Yusupov, M. , Yusupova, G.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 3.7 Å
Hibernating ribosome from staphylococcus aureus (rotated state)
Ayupov, R. , Hashem, Y. , Khusainov, I. , Kieffer, B. , Myasnikov, A. , Simonetti, A. , Usachev, K. , Validov, S. , Vicens, Q. , Yusupov, M. , Yusupova, G.
Primary Citation of Related Structures: 5ND9
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 23S ribosomal RNA | a | 2923 | NA | GAUUAAGUUAUUAAGGGCGCACGGUGGAUGCCUUGGCACUAGAAGCCGAUGAAGGACGUUACUAACGACGAUAUGCUUUGGGGAGCUGUAAGUAAGCUUUGAUCCAGAGAUUUCCGAAUGGGGAAACCCAGCAUGAGUUAUGUCAUGUUAUCGAUAUGUGAAUACAUAGCAUAUCAGAAGGCACACCCGGAGAACUGAAACAUCUUAGUACCCGGAGGAAGAGAAAGAAAAUUCGAUUCCCUUAGUAGCGGCGAGCGAAAUGGGAAGAGCCCAAACCAACAAGCUUGCUUGUUGGGGUUGUAGGACACUCUAUACGGAGUUACAAAGGACGACAUUAGACGAAUCAUCUGGAAAGAUGAAUCAAAGAAGGUAAUAAUCCUGUAGUCGAAAAUGUUGUCUCUCUUGAGUGGAUCCUGAGUACGACGGAGCACGUGAAAUUCCGUCGGAAUCUGGGAGGACCAUCUCCUAAGGCUAAAUACUCUCUAGUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGUGAAAAGCACCCCGGAAGGGGAGUGAAAUAGAACCUGAAACCGUGUGCUUACAAGUAGUCAGAGCCCGUUAAUGGGUGAUGGCGUGCCUUUUGUAGAAUGAACCGGCGAGUUACGAUUUGAUGCAAGGUUAAGCAGUAAAUGUGGAGCCGUAGCGAAAGCGAGUCUGAAUAGGGCGUUUAGUAUUUGGUCGUAGACCCGAAACCAGGUGAUCUACCCUUGGUCAGGUUGAAGUUCAGGUAACACUGAAUGGAGGACCGAACCGACUUACGUUGAAAAGUGAGCGGAUGAACUGAGGGUAGCGGAGAAAUUCCAAUCGAACCUGGAGAUAGCUGGUUCUCUCCGAAAUAGCUUUAGGGCUAGCCUCAAGUGAUGAUUAUUGGAGGUAGAGCACUGUUUGGACGAGGGGCCCCUCUCGGGUUACCGAAUUCAGACAAACUCCGAAUGCCAAUUAAUUUAACUUGGGAGUCAGAACAUGGGUGAUAAGGUCCGUGUUCGAAAGGGAAACAGCCCAGACCACCAGCUAAGGUCCCAAAAUAUAUGUUAAGUGGAAAAGGAUGUGGCGUUGCCCAGACAACUAGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAGUGCGUAAUAGCUCACUAGUCGAGUGACACUGCGCCGAAAAUGUACCGGGGCUAAACAUAUUACCGAAGCUGUGGAUUGUCCUUUGGACAAUGGUAGGAGAGCGUUCUAAGGGCGUUGAAGCAUGAUCGUAAGGACAUGUGGAGCGCUUAGAAGUGAGAAUGCCGGUGUGAGUCGCGAAAGACGGGUGAGAAUCCCGUCCACCGAUUGACUAAGGUUUCCAGAGGAAGGCUCGUCCGCUCUGGGUUAGUCGGGUCCUAAGCUGAGGCCGACAGGCGUAGGCGAUGGAUAACAGGUUGAUAUUCCUGUACCACCUAUAAUCGUUUUAAUCGAUGGGGGGACGCAGUAGGAUAGGCGAAGCGUGCGAUUGGAUUGCACGUCUAAGCAGUAAGGCUGAGUAUUAGGCAAAUCCGGUACUCGUUAAGGCUGAGCUGUGAUGGGGAGAAGACAUUGAGUCUUCGAGUCGUUGAUUUCACACUGCCGAGAAAAGCCUCUAGAUAGAAAAUAGGUGCCCGUACCGCAAACCGACACAGGUAGUCAAGAUGAGAAUUCUAAGGUGAGCGAGCGAACUCUCGUUAAGGAACUCGGCAAAAUGACCCCGUAACUUCGGGAGAAGGGGUGCUCUUUAGGGUUAACGCCCAGAAGAGCCGCAGUGAAUAGGCCCAAGCGACUGUUUAUCAAAAACACAGGUCUCUGCUAAACCGUAAGGUGAUGUAUAGGGGCUGACGCCUGCCCGGUGCUGGAAGGUUAAGAGGAGUGGUUAGCUUCUGCGAAGCUACGAAUCGAAGCCCCAGUAAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCCGCACGAAAGGCGUAACGAUUUGGGCACUGUCUCAACGAGAGACUCGGUGAAAUCAUAGUACCUGUGAAGAUGCAGGUUACCCGCGACAGGACGGAAAGACCCCGUGGAGCUUUACUGUAGCCUGAUAUUGAAAUUCGGCACAGCUUGUACAGGAUAGGUAGGAGCCUUUGAAACGUGAGCGCUAGCUUACGUGGAGGCGCUGGUGGGAUACUACCCUAGCUGUGUUGGCUUUCUAACCCGCACCACUUAUCGUGGUGGGAGACAGUGUCAGGCGGGCAGUUUGACUGGGGCGGUCGCCUCCUAAAAGGUAACGGAGGCGCUCAAAGGUUCCCUCAGAAUGGUUGGAAAUCAUUCAUAGAGUGUAAAGGCAUAAGGGAGCUUGACUGCGAGACCUACAAGUCGAGCAGGGUCGAAAGACGGACUUAGUGAUCCGGUGGUUCCGCAUGGAAGGGCCAUCGCUCAACGGAUAAAAGCUACCCCGGGGAUAACAGGCUUAUCUCCCCCAAGAGUUCACAUCGACGGGGAGGUUUGGCACCUCGAUGUCGGCUCAUCGCAUCCUGGGGCUGUAGUCGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGUACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCCCUAUCCGUCGUGGGCGUAGGAAAUUUGAGAGGAGCUGUCCUUAGUACGAGAGGACCGGGAUGGACAUACCUCUGGUGUACCAGUUGUCGUGCCAACGGCAUAGCUGGGUAGCUAUGUGUGGACGGGAUAAGUGCUGAAAGCAUCUAAGCAUGAAGCCCCCCUCAAGAUGAGAUUUCCCAACUUCGGUUAUAAGAUCCCUCAAAGAUGAUGAGGUUAAUAGGUUCGAGGUGGAAGCAUGGUGACAUGUGGAGCUGACGAAUACUAAUCGAUCGAAGACUUAAUCAA |
| 5S ribosomal RNA | b | 114 | NA | UCUGGUGACUAUAGCAAGGAGGUCACACCUGUUCCCAUGCCGAACACAGAAGUUAAGGUCUUUAGCGACGAUGGUAGCCAACUUACGUUCCGCUAGAGUAGAACGUUGCCAGGC |
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 30S ribosomal protein S10 | J | 102 | Staphylococcus Aureus (Strain Nctc 8325) , Staphylococcus Aureus Subsp. Aureus Nctc 8325 | MAKQKIRIRLKAYDHRVIDQSAEKIVETAKRSGADVSGPIPLPTEKSVYTIIRAVHMYKDSREQFEQRTHKRLIDIVNPTPKTVDALMGLNLPSGVDIEIKL |
| 30S ribosomal protein S11 | K | 129 | Staphylococcus Aureus (Strain Nctc 8325) , Staphylococcus Aureus Subsp. Aureus Nctc 8325 | MARKQVSRKRRVKKNIENGVAHIRSTFNNTIVTITDEFGNALSWSSAGALGFKGSKKSTPFAAQMASETASKSAMEHGLKTVEVTVKGPGPGRESAIRALQSAGLEVTAIRDVTPVPHNGCRPPKRRRV |
| 30S ribosomal protein S12 | L | 137 | Staphylococcus Aureus (Strain Nctc 8325) , Staphylococcus Aureus Subsp. Aureus Nctc 8325 | MPTINQLVRKPRQSKIKKSDSPALNKGFNSKKKKFTDLNSPQKRGVCTRVGTMTPKKPNSALRKYARVRLSNNIEINAYIPGIGHNLQEHSVVLVRGGRVKDLPGVRYHIVRGALDTSGVDGRRQGRSLYGTKKPKN |
| 50S ribosomal protein L13 | M | 145 | Staphylococcus Aureus (Strain Nctc 8325) , Staphylococcus Aureus Subsp. Aureus Nctc 8325 | MRQTFMANESNIERKWYVIDAEGQTLGRLSSEVASILRGKNKVTYTPHVDTGDYVIVINASKIEFTGNKETDKVYYRHSNHPGGIKSITAGELRRTNPERLIENSIKGMLPSTRLGEKQGKKLFVYGGAEHPHAAQQPENYELRG |
| 50S ribosomal protein L14 | N | 122 | Staphylococcus Aureus (Strain Nctc 8325) , Staphylococcus Aureus Subsp. Aureus Nctc 8325 | MIQQETRLKVADNSGAREVLTIKVLGGSGRKTANIGDVIVCTVKNATPGGVVKKGDVVKAVIVRTKSGVRRNDGSYIKFDENACVIIRDDKGPRGTRIFGPVARELREGNFMKIVSLAPEVL |
| 50S ribosomal protein L15 | O | 146 | Staphylococcus Aureus (Strain Nctc 8325) , Staphylococcus Aureus Subsp. Aureus Nctc 8325 | MKLHELKPAEGSRKERNRVGRGVATGNGKTSGRGHKGQKARSGGGVRPGFEGGQLPLFRRLPKRGFTNINRKEYAIVNLDQLNKFEDGTEVTPALLVESGVVKNEKSGIKILGNGSLDKKLTVKAHKFSASAAEAIDAKGGAHEVI |
| 50S ribosomal protein L16 | P | 144 | Staphylococcus Aureus (Strain Nctc 8325) , Staphylococcus Aureus Subsp. Aureus Nctc 8325 | MLLPKRVKYRRQHRPKTTGRSKGGNYVTFGEFGLQATTTSWITSRQIESARIAMTRYMKRGGKVWIKIFPHTPYTKKPLEVRMGAGKGAVEGWIAVVKPGRILFEVAGVSEEVAREALRLASHKLPVKTKFVKREELGGETNES |
| 50S ribosomal protein L17 | Q | 122 | Staphylococcus Aureus (Strain Nctc 8325) , Staphylococcus Aureus Subsp. Aureus Nctc 8325 | MGYRKLGRTSDQRKAMLRDLATSLIISERIETTEARAKEVRSVVEKLITLGKKGDLASRRNAAKTLRNVEILNEDETTQTALQKLFGEIAERYTERQGGYTRILKQGPRRGDGAESVIIELV |
| 50S ribosomal protein L18 | R | 119 | Staphylococcus Aureus (Strain Nctc 8325) , Staphylococcus Aureus Subsp. Aureus Nctc 8325 | MISKIDKNKVRLKRHARVRTNLSGTAEKPRLNVYRSNKHIYAQIIDDNKGVTLAQASSKDSDIATTATKVELATKVGEAIAKKAADKGIKEIVFDRGGYLYHGRVKALAEAARESGLEF |
| 50S ribosomal protein L19 | S | 116 | Staphylococcus Aureus (Strain Nctc 8325) , Staphylococcus Aureus Subsp. Aureus Nctc 8325 | MTNHKLIEAVTKSQLRTDLPSFRPGDTLRVHVRIIEGTRERIQVFEGVVIKRRGGGVSETFTVRKISSGVGVERTFPLHTPKIEKIEVKRRGKVRRAKLYYLRSLRGKAARIQEIR |
| 50S ribosomal protein L20 | T | 118 | Staphylococcus Aureus (Strain Nctc 8325) , Staphylococcus Aureus Subsp. Aureus Nctc 8325 | MPRVKGGTVTRARRKKTIKLAKGYFGSKHTLYKVAKQQVMKSGQYAFRDRRQRKRDFRKLWITRINAAARQHEMSYSRLMNGLKKAGIDINRKMLSEIAISDEKAFAQLVTKAKDALK |
| 50S ribosomal protein L21 | U | 102 | Staphylococcus Aureus (Strain Nctc 8325) , Staphylococcus Aureus Subsp. Aureus Nctc 8325 | MFAIIETGGKQIKVEEGQEIFVEKLDVNEGDTFTFDKVLFVGGDSVKVGAPTVEGATVTATVNKQGRGKKITVFTYKRRKNSKRKKGHRQPYTKLTIDKINA |
| 50S ribosomal protein L22 | V | 117 | Staphylococcus Aureus (Strain Nctc 8325) , Staphylococcus Aureus Subsp. Aureus Nctc 8325 | MEAKAVARTIRIAPRKVRLVLDLIRGKNAAEAIAILKLTNKASSPVIEKVLMSALANAEHNYDMNTDELVVKEAYANEGPTLKRFRPRAQGRASAINKRTSHITIVVSDGKEEAKEA |
| 30S ribosomal protein S4 | D | 200 | Staphylococcus Aureus (Strain Nctc 8325) , Staphylococcus Aureus Subsp. Aureus Nctc 8325 | MARFRGSNWKKSRRLGISLSGTGKELEKRPYAPGQHGPNQRKKLSEYGLQLREKQKLRYLYGMTERQFRNTFDIAGKKFGVHGENFMILLASRLDAVVYSLGLARTRRQARQLVNHGHILVDGKRVDIPSYSVKPGQTISVREKSQKLNIIVESVEINNFVPEYLNFDADSLTGTFVRLPERSELPAEINEQLIVEYYSR |
| 30S ribosomal protein S5 | E | 166 | Staphylococcus Aureus (Strain Nctc 8325) , Staphylococcus Aureus Subsp. Aureus Nctc 8325 | MARREEETKEFEERVVTINRVAKVVKGGRRFRFTALVVVGDKNGRVGFGTGKAQEVPEAIKKAVEAAKKDLVVVPRVEGTTPHTITGRYGSGSVFMKPAAPGTGVIAGGPVRAVLELAGITDILSKSLGSNTPINMVRATIDGLQNLKNAEDVAKLRGKTVEELYN |
| 30S ribosomal protein S6 | F | 98 | Staphylococcus Aureus (Strain Nctc 8325) , Staphylococcus Aureus Subsp. Aureus Nctc 8325 | MRTYEVMYIVRPNIEEDAKKALVERFNGILATEGAEVLEAKDWGKRRLAYEINDFKDGFYNIVRVKSDNNKATDEFQRLAKISDDIIRYMVIREDEDK |
| 30S ribosomal protein S7 | G | 156 | Staphylococcus Aureus (Strain Nctc 8325) , Staphylococcus Aureus Subsp. Aureus Nctc 8325 | MPRKGSVPKRDVLPDPIHNSKLVTKLINKIMLDGKRGTAQRILYSAFDLVEQRSGRDALEVFEEAINNIMPVLEVKARRVGGSNYQVPVEVRPERRTTLGLRWLVNYARLRGEKTMEDRLANEILDAANNTGGAVKKREDTHKMAEANKAFAHYRW |
| 30S ribosomal protein S8 | H | 132 | Staphylococcus Aureus (Strain Nctc 8325) , Staphylococcus Aureus Subsp. Aureus Nctc 8325 | MTMTDPIADMLTRVRNANMVRHEKLELPASNIKKEIAEILKSEGFIKNVEYVEDDKQGVLRLFLKYGQNDERVITGLKRISKPGLRVYAKASEMPKVLNGLGIALVSTSEGVITDKEARKRNVGGEIIAYVW |
| 30S ribosomal protein S3 | C | 217 | Staphylococcus Aureus (Strain Nctc 8325) , Staphylococcus Aureus Subsp. Aureus Nctc 8325 | MGQKINPIGLRVGIIRDWEAKWYAEKDFASLLHEDLKIRKFIDNELKEASVSHVEIERAANRINIAIHTGKPGMVIGKGGSEIEKLRNKLNALTDKKVHINVIEIKKVDLDARLVAENIARQLENRASFRRVQKQAITRAMKLGAKGIKTQVSGRLGGADIARAEQYSEGTVPLHTLRADIDYAHAEADTTYGKLGVKVWIYRGEVLPTKNTSGGGK |
| 50S ribosomal protein L23 | W | 91 | Staphylococcus Aureus (Strain Nctc 8325) , Staphylococcus Aureus Subsp. Aureus Nctc 8325 | MEARDILKRPVITEKSSEAMAEDKYTFDVDTRVNKTQVKMAVEEIFNVKVASVNIMNYKPKKKRMGRYQGYTNKRRKAIVTLKEGSIDLFN |
| 50S ribosomal protein L24 | X | 105 | Staphylococcus Aureus (Strain Nctc 8325) , Staphylococcus Aureus Subsp. Aureus Nctc 8325 | MHIKKGDNVKVIAGKDKGKEGKVIATLPKKDRVVVEGVNIMKKHQKPTQLNPEGGILETEAAIHVSNVQLLDPKTNEPTRVGYKFVDGKKVRIAKKSGEEIKSNN |
| 50S ribosomal protein L25 | Y | 217 | Staphylococcus Aureus (Strain Nctc 8325) , Staphylococcus Aureus Subsp. Aureus Nctc 8325 | MASLKSIIRQGKQTRSDLKQLRKSGKVPAVVYGYGTKNVSVKVDEVEFIKVIREVGRNGVIELGVGSKTIKVMVADYQFDPLKNQITHIDFLAINMSEERTVEVPVQLVGEAVGAKEGGVVEQPLFNLEVTATPDNIPEAIEVDITELNINDSLTVADVKVTGDFKIENDSAESVVTVVAPTEEPTEEEIEAMEGEQQTEEPEVVGESKEDEEKTEE |
| 50S ribosomal protein L27 | Z | 94 | Staphylococcus Aureus (Strain Nctc 8325) , Staphylococcus Aureus Subsp. Aureus Nctc 8325 | MLKLNLQFFASKKGVSSTKNGRDSESKRLGAKRADGQFVTGGSILYRQRGTKIYPGENVGRGGDDTLFAKIDGVVKFERKGRDKKQVSVYAVAE |
| 50S ribosomal protein L28 | 0 | 62 | Staphylococcus Aureus (Strain Nctc 8325) , Staphylococcus Aureus Subsp. Aureus Nctc 8325 | MGKQCFVTGRKASTGNRRSHALNSTKRRWNANLQKVRILVDGKPKKVWVSARALKSGKVTRV |
| 50S ribosomal protein L29 | 1 | 69 | Staphylococcus Aureus (Strain Nctc 8325) , Staphylococcus Aureus Subsp. Aureus Nctc 8325 | MKAKEIRDLTTSEIEEQIKSSKEELFNLRFQLATGQLEETARIRTVRKTIARLKTVAREREIEQSKANQ |
| 50S ribosomal protein L30 | 2 | 59 | Staphylococcus Aureus (Strain Nctc 8325) , Staphylococcus Aureus Subsp. Aureus Nctc 8325 | MAKLQITLTRSVIGRPETQRKTVEALGLKKTNSSVVVEDNPAIRGQINKVKHLVTVEEK |
| 50S ribosomal protein L31 type B | 3 | 84 | Staphylococcus Aureus (Strain Nctc 8325) , Staphylococcus Aureus Subsp. Aureus Nctc 8325 | MKQGIHPEYHQVIFLDTTTNFKFLSGSTKTSSEMMEWEDGKEYPVIRLDISSDSHPFYTGRQKFAAADGRVERFNKKFGLKSNN |
| 50S ribosomal protein L32 | 4 | 58 | Staphylococcus Aureus (Strain Nctc 8325) , Staphylococcus Aureus Subsp. Aureus Nctc 8325 | MAVPKRRTSKTRKNKRRTHFKISVPGMTECPNCGREYKLSHRVCKNCGSYNGEEVAAK |
| 50S ribosomal protein L33 2 | 5 | 49 | Staphylococcus Aureus (Strain Nctc 8325) , Staphylococcus Aureus Subsp. Aureus Nctc 8325 | MRVNVTLACTECGDRNYITTKNKRNNPERVEMKKFCSRENKQTLHRETK |
| 50S ribosomal protein L34 | 6 | 45 | Staphylococcus Aureus (Strain Nctc 8325) , Staphylococcus Aureus Subsp. Aureus Nctc 8325 | MVKRTYQPNKRKHSKVHGFRKRMSTKNGRKVLARRRRKGRKVLSA |
| 50S ribosomal protein L35 | 7 | 66 | Staphylococcus Aureus (Strain Nctc 8325) , Staphylococcus Aureus Subsp. Aureus Nctc 8325 | MPKMKTHRGAAKRVKRTASGQLKRSRAFTSHLFANKSTKQKRQLRKARLVSKSDMKRVKQLLAYKK |
| 50S ribosomal protein L36 | 8 | 37 | Staphylococcus Aureus (Strain Nctc 8325) , Staphylococcus Aureus Subsp. Aureus Nctc 8325 | MKVRPSVKPICEKCKVIKRKGKVMVICENPKHKQRQG |
| 30S ribosomal protein S9 | I | 132 | Staphylococcus Aureus (Strain Nctc 8325) , Staphylococcus Aureus Subsp. Aureus Nctc 8325 | MTLAQVEYRGTGRRKNSVARVRLVPGEGNITVNNRDVREYLPFESLILDLNQPFDVTETKGNYDVLVNVHGGGFTGQAQAIRHGIARALLEADPEYRGSLKRAGLLTRDPRMKERKKPGLKAARRSPQFSKR |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2017-03-07 Deposition Author(s): Ayupov, R. , Hashem, Y. , Khusainov, I. , Kieffer, B. , Myasnikov, A. , Simonetti, A. , Usachev, K. , Validov, S. , Vicens, Q. , Yusupov, M. , Yusupova, G.