Cryo-em structure of t. kodakarensis 70s ribosome
PDB DOI: 10.2210/pdb6skf/pdb
Classification: RIBOSOME Organism(s): Thermococcus Kodakarensis
Deposited: 2019-08-15 Deposition Author(s): Matzov, D. , Meier, J.L. , Santangelo, T. , Sas-Chen, A. , Schwartz, S. , Shalev-Benami, M. , Thomas, J.M.
Cryo-em structure of t. kodakarensis 70s ribosome
Matzov, D. , Meier, J.L. , Santangelo, T. , Sas-Chen, A. , Schwartz, S. , Shalev-Benami, M. , Thomas, J.M.
Primary Citation of Related Structures: 6SKF
Nucleic Acids / Hybrid | ||||
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Molecule | Chains | Sequence Length | Organism | Sequence |
16S rRNA | aa | 1498 | NA | AUUCNGGUUGAUCCUGCCGGAGGCCACUGCUAUGGGGGUCNGACUAAGCCAUGCGAGUCAUGGGGCGCGCUCUGCGCGCACCGGCGGACGGCUCAGUAACACGUCGGUAACCUACCCUCGGGAGGGGGAUAACCCNGGGAAACUGGGGCUAAUCCCCCAUAGGCCUGAGGUACUGGAAGGUCCUCAGGCCGAAAGGGGCAUCUGCCCGCCCGAGGAUGGGCCGGCGGCCGAUUAGGUAGUUGGUGGGGUAACGGCCCACCAAGCCGAAGAUCGGUACGGGCCAUGAGAGUGGGAGCCNGGAGAUGGACACUGAGACACGGGUCCAGGCCCUACGGGGCGCAGCAGGCGCGAAACCUCNGCAAUGCGGGCAACNGCGACGGGGGGACCCCCAGUGCCGUGGCAUAGCCACGGCUUUUCCGGAGUGUAAAAAGCUCCGGGAAUAAGGGCUGGGCAAGGCNGGUGGCAGCCGCCGCGGUAAUACCGGCGGCCCGAGUGGUGGCNGCUAUUAUUGGGCCUAAAGCGUCNGUAGCCGGGCCCGUAAGUCCCUGGCGAAAUCCCACGGCUCAACNGUGGGGCUUGCUGGGGAUACUGCGGGCCUUGGGACNGGGAGAGGCCGGGGGUACCCCUGGGGUAGGGGUGAAAUCCUAUAAUCCCAGGGGGACCGCCAGUGGCGAAGGCGCCNGGCUGGAACGGGUCNGACGGUGAGGGACGAAGGCCAGGGGAGCGAACNGGAUUAGAUACCCGGGUAGUCCUGGCUGUAAAGGAUGCGGGCUAGGUGUCGGGCGAGCUUCGAGCUCGCCCGGUGCCGGAGGGAAGCNGUUAAGCCNGCCGCCUGGGGAGUACGGCNGCAAGGCUGAAACUUAAAGGAAUUGGCGGGGGAGCACUACAAGGGGUGGAGCGUGCGGUUUAAUUGGAUUCAACGCCGGGAACCUCACCGGGGGCGACGGCAGGAUGAAGGCCAGGCUGAAGGUCUUGCCGGACACGCCGAGAGGAGGUGCAUGGCCGCNGUCAGCUCGUACCGUGAGGCGUCCACUUAAGUGUGGUAACGAGCGAGACCCGCGCCCCCAGUUGCCAGUCCUCCCCGCUGGGGAGGAGGCACUCUGGGGGGACCGCCGGCGAUAAGCCGGAGGAAGGAGCGGGCGACGGUAGGUCAGUAUGCCCCGAAACCCCCGGGCUACACGCGCGCUACAAUGGGCGGGACAAUGGGAUCCGACCCNGAAAGGGGAAGGGAAUCCCCUAAACCCGCCCUCAGUUCGGAUCGCGGGCUGCAACUCGCCCGCGUGAAGCUGGAAUCCCUAGUACCCGCGUGUCAUCAUCGCGCGGCGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUCACUCCACCCGAGCGGGGUCCGGGUGAGGCCUGGUCUCCCUUCGGGGAGGCCGGGUCGAGCCUGGGCUCCGUGAGGGGGGAGAAGUCGUAACAAGGUAGCNGUAGGGGAACCUACGGCUCGAUCACCUCCUAUCGCCGGA |
Proteins | ||||
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Molecule | Chains | Sequence Length | Organism | Sequence |
30S ribosomal protein S8 | AJ | 130 | Thermococcus Kodakarensis | MTLLDPLANALSHITNSERVGKKEVYIKPASKLIGEVLRVMLENGYIGEFELIDDGRAGIYRVQLIGKINKAGAIKPRFPVKARDYEKWEKRFLPAFEFGILIVSTSQGVMTHKEALEKGIGGRLIAYVY |
30S ribosomal protein S8e | AK | 130 | Thermococcus Kodakarensis | MAIWQGRSLKKPSGGRIILARKKRKRELGREPANTKVGEDREKRKIIRTYGGNRKVRLVEALYANVFEGGKGKKVKILNVVENPANRQYARRNIITKGAIIETEIGKAIVTSRPGQDGVVNAVLIKEENA |
30S ribosomal protein S9 | AL | 135 | Thermococcus Kodakarensis | MRVIQTAGKRKTAVARATIREGKGRVRINHKPVEIIEPEIARFTIMEPLILAGEEIVSRVDIDVKVEGGGFMGQAEAARVAIARALVEWTNDMNLKEKFMKYDRTMLVGDSRRTEPHKPNRSTKGPRAKRQKSYR |
30S ribosomal protein S10 | AM | 102 | Thermococcus Kodakarensis | MQKARIKLASTNIKALNEVTDQIKQIAERTGVRMSGPIPLPTKRIRITTRKSPDGEGSATFDRFELRVHKRLVDIEADERAMRQIMRIRVPEDVTIEIELIS |
30S ribosomal protein S11 | AN | 140 | Thermococcus Kodakarensis | MSEEQTTQVNIKKKEKWGVAHIYSSYNNTIIHITDLTGAETISRWSGGMVVKADRDEPSPYAAMIAARRAAEEAMEKGITGVHIKVRAPGGSKSKSPGPGAQAAIRALSRAGLRIGRVEDVTPIPHDGTRPKGGRRGRRV |
30S ribosomal protein S12 | AO | 147 | Thermococcus Kodakarensis | MAGKKAPYGEFAGRKLKLKRKKFRWSDIRYKRRVLRLKEKSDPLEGAPQARGIVLEKIAVEAKQPNSAMRKAVRVQLIKNGKVVTAFTPGDGAINHIDEHDEVIIEGIGGPKGGSMGDIPGIRYKVVKVNRVSLKELVKGRKEKPRR |
30S ribosomal protein S13 | AP | 149 | Thermococcus Kodakarensis | MTENFRHIVRVAGVDIDGHKQVRWALTGIKGIGINFATMVLRVAGIDPFMKAGYLTDEQVKKIEEILADPVAHGIPAWAVNRPKDYETGKDMHLITAKLVMAWREDVNRLRRIRAYRGIRHELGLPVRGQRTRSNFRHGTTVGVSRRKK |
30S ribosomal protein S15 | AQ | 151 | Thermococcus Kodakarensis | MARIHARKRGKSGSKRPPRTAPPAWVEYTAEEVEALVVKLRKEGYSTAMIGTILRDQYGIPSVKLITGKKITKILEENGLAPEIPEDLMFLIRRAVNLRKHLEQHPKDKHSRRGLQLIESKIRRLVKYYRRTGKLPAKWRYDPEQAKLLVR |
30S ribosomal protein S14 type Z | AR | 56 | Thermococcus Kodakarensis | MAKADYNKRKPRKFGKGARRCMRCGQYGPIIRIHGLMLCRHCFREVAPKLGFKKYE |
30S ribosomal protein S17 | AS | 114 | Thermococcus Kodakarensis | MREIGLRVQPPAEVCNDPKCPWHGNLKIHGRYVEGIVVSDKGKKTVVVERQYYHYLKKYERYELRKSKVHAHNPECINAKVGDKVLIAETRPISKTKSWVVVAVLQRAERAEEV |
30S ribosomal protein S2 | AB | 201 | Thermococcus Kodakarensis | MEEYLVPLDQYLAAGVHIGTQQKTKDMKKFIYRVRQDGLYVLDVRKTDERLRVAGKFLAKFDPESILAVSVRLYGQRPVKKFGEVTGAKAIPGRFLPGTMTNPQVKNFIEPDVLIVTDPRADHQALKEAVEIGIPIVALVDTENFLSYVDIAIPTNNKGRKALALIYWILAREVLYNRKEIESREDFKIPVEDFEMRIIRT |
30S ribosomal protein S17e | AT | 67 | Thermococcus Kodakarensis | MGNIKQTFIKRTARELFDRYPDKFTRDFEHNKKMVAELTNVTSKTIRNRIAGYITRLVRMKEEGKIL |
30S ribosomal protein S19 | AU | 133 | Thermococcus Kodakarensis | MARKKEFRYRGYTLDELLNMSLEEFAKLLPSRQRRSLKRGLSPEQKKLLRKIRLAKKGKYNKPIRTHSRDMIVLPEMVGMTIHVYNGKEFVPVEIKEEMIGHYLGEFAMTRKVVQHGSPGVGATRSSMFVAVK |
30S ribosomal protein S19e | AV | 150 | Thermococcus Kodakarensis | MATVYDVPGDLLVERVAKALKEVPEIKPPEWAPFVKTGRHKERLPEQEDWWYYRVASVFRKVYIDGPVGIERLRTWYGGRKNRGHAPEHFYKAGGSIIRKALQQLEAAGFVQKVPGEGRIVTPKGQSFLDKIATELKKELEEQIPELKKY |
30S ribosomal protein S24e | AW | 98 | Thermococcus Kodakarensis | MEIKVTEIRENKLLGRKEIYFDVLHEGEPTPSREAVKGKLVAMLDLDPNTTVIQYIRSYFGSNVSKGYAKAYETRERMLYIEPEYILVRDGLVQKQEE |
30S ribosomal protein S27e | AX | 65 | Thermococcus Kodakarensis | MALPKNLIPMPRSRFLRVKCIDCGNEQIVFSHPATPVRCLVCGATLVEPTGGKGIIKAKVLEVEE |
30S ribosomal protein S28e | AY | 70 | Thermococcus Kodakarensis | MSDEGYPAEVIEIVGRTGVTGGVTQVKVRILEGRDKGRVIRRNVKGPVRVGDIVILRETEREAREIRRRR |
Predicted zinc-ribbon RNA-binding protein involved in translation | AZ | 62 | Thermococcus Kodakarensis | MFAVEMKFEVPVCTSCGKEITPREHATHFVCPNCGEAIIWRCESCRVLSVPYKCPKCGWEGP |
50S ribosomal protein L30 | BA | 155 | Thermococcus Kodakarensis | MAKLALIRLRSGIRARGEVRDTLAMLRLHRINHLVIVDDTPSYRGMIQKVKDYITWGEIDKETLAKLLRKRGRLIGNKPITDEYVKEKLGMTIEEFAEKVVNGEMKLRDLPNIKPVFRLHPPRGGLKGSKKRSFKEGGALGYRGEKINELIERML |
50S ribosomal protein L30e | BB | 102 | Thermococcus Kodakarensis | MVDFAFELRKVQDTGKIVMGAKKSIHLAKVGGAKLIIVARNARPDIKEDIYYYAKLSGIPVYEFEGTSVELGTLLGRPHTVSALAVIDPGESKILALAGGKE |
50S ribosomal protein L31e | BC | 90 | Thermococcus Kodakarensis | MPIKPGEEVIFVVPINKIKKRVPRWKRAPRAARFVREWIARHAKADEVIIGTDVNEKIWERGAEKPPGKLRVKVVVEESEGKRIARVSLA |
30S ribosomal protein S3 | AC | 209 | Thermococcus Kodakarensis | MAIERYFIKEGVKEMLIDEFLEKELRRAGYGGLDIKKTPLGTKVTIFAANPGYVIGRGGRRIRELTRILEKQFGLENPQIEVEEIKNPYLNAKVQAVRLAQALERGIHFRRAAYSAIRAIMRNGARGVEIRLSGKLTGERAKSVRFYQGYLAKVGNPAETLVSRGYAQAQLKLGVIGVKVSIMPPDAKLPDEIEIKEIVEEEVSANEAQ |
50S ribosomal protein L32e | BD | 125 | Thermococcus Kodakarensis | MNEKARLLRIRAKLKRKKPRFLRQEWWRYPKFKNDPKWRRPKGIDSKMRLKKKGKPRSPSIGWSSPKAVRGLHPSGYEEVLVHNVKELEAIDPTRQAARIAGTVGARKREMILARAKELGVKVLN |
50S ribosomal protein L34e | BE | 90 | Thermococcus Kodakarensis | MKPMYRSRSWRRKYVRTPGGRTVIHFERRKPKVAHCAMCGRPLNGVPRGRPSELRKLPKTKKRPERPYPNLCPSCMRKVMKAQVRASITA |
50S ribosomal protein L5 | BF | 183 | Thermococcus Kodakarensis | MQINREAILADWEAHPMRKPRIAKVTINIGVGESGERLTKAETMLEQLVGQKPIRRRAKQTNRDFGIRRGEPIAVKVTLRGEKAYQMLDRLLEAVDRKLKASNFDEHGNFCFGIQEHINIPGVEYDPEIGIFGMDVCVTLERPGFRVAKRKRQRRKIPTKHKLTKEEGIVFAMEELKAKVEGL |
50S ribosomal protein L37Ae | BG | 86 | Thermococcus Kodakarensis | MGRTTKVGSAGRFGPRYGLKIRRRVAAVEARMKQKHVCPVCGRKAVRRISTGIWQCQKCGATFAGGAYLPTTPAGKVAKRVTASKA |
50S ribosomal protein L37e | BH | 63 | Thermococcus Kodakarensis | MGAGTAPKGKRNRTPTHIRCRRCGRRAFNVKKGYCAACGFGRSRRMRKYSWSHKWRKKRNLSY |
50S ribosomal protein L39e | BI | 51 | Thermococcus Kodakarensis | MARNKPFAKKLRLAKAAKQNRRVPVWVIVKTNRKVITHPKRRHWRRTKLKE |
50S ribosomal protein L40e | BJ | 51 | Thermococcus Kodakarensis | MARFPEAEARIFRKLVCMRCGATNPWGAKKCRKCGYKGLRPKAREPRGGGR |
LSU ribosomal protein L41E | BK | 37 | Thermococcus Kodakarensis | MKRRPRKWKKKGRMRWKWIKKRIRRLKRQRRKERGLI |
50S ribosomal protein L44e | BL | 94 | Thermococcus Kodakarensis | MKYPKQIRTYCPFCKRHTIHKVEKVKKRPRSELSAGQRRFRRKLKGYTGFPRPNPAGREKPVKKLDLRFRCTVCGKAHTRGQGFRVKKFELVEV |
50S ribosomal protein L14e | BM | 83 | Thermococcus Kodakarensis | MPAIEVGRIAVVIAGRRAGQKVVVADIIDKNFVLVTGAGLNKVKRRRMNVKHLEPLPERVNIQRGASDEEIKAALEGAGISLE |
50S ribosomal protein L14e | BN | 83 | Thermococcus Kodakarensis | MPAIEVGRIAVVIAGRRAGQKVVVADIIDKNFVLVTGAGLNKVKRRRMNVKHLEPLPERVNIQRGASDEEIKAALEGAGISLE |
50S ribosomal protein L15 | BO | 148 | Thermococcus Kodakarensis | MIRRRKKVRKLRGSHTHGWGCKKKHRGGGSKGGRGMAGTGKRKDQKWTWTIKYAPDRLGKRGFHRPKAVQYIPKVINLNDIDENFELFKDAGIIYEEDGKLVFDATALGVDKILGTGKLTRALVVKAYYVTPKAEEKIKAAGGEVLLA |
30S ribosomal protein S3Ae | AD | 200 | Thermococcus Kodakarensis | MARGNPRKRAAAAKDKWKMKEWYIVYAPDFFGSKEIGLTPADDPEKVIGRVIETTLKDLTGDFTKGHVKLYFQVYDVKGQNAYTKFKGHTLARSYIRSLVRRRTTRVDGIFNITTKDGYKLRVMGMVIAYRRIQTSQERAIRKIIQDIIYKKAEELNFADFVLQSVNGQIASEIAKEARKIYPIKRAEVRKIKVLAEPSA |
50S ribosomal protein L15e | BP | 194 | Thermococcus Kodakarensis | MGMYKYIREAWKSPKKSYVGELLKKRMIQWRRDPVVKRIERPTRLDRARSLGYQAKQGYVVVRVRVRRGGRKRPRWKGGRKPSKMGMVKYSPKKSLQWIAEEKAARKFPNLEVLNSYWVGEDGMYKWFEVIMVDPHHPVIKSDPKIAWIAGKAHKGRVFRGLTSAGKRSRGLLNKGKGAEKVRPSIRAHQGKGK |
50S ribosomal protein L18 | BQ | 201 | Thermococcus Kodakarensis | MAHGPRYRVPFRRRREGKTNYHKRLKLLKSKKPRLVVRKTLNHHIAQIVVYDPKGDKTLVSAHTMELMRDFGWKGHGGNTPSAYLLGLLIGYKAKQAGIEEAILDIGLHPPTRGSSIFAVLKGAVDAGLNVPHSEEIYPEDYRINGEHIANYAKALKEEDEALYRKQFSGYLVKGLEPEKLPEHFEEVKAKIIEKFEGARE |
50S ribosomal protein L18e | BR | 121 | Thermococcus Kodakarensis | MVKRTGPTDINLRRLIRTLRKKSNEEGVKIWKDIAWRLERPRRQRAEVNISKINRYTKEGDVVIVPGSVLGAGRLEHKVVVAAWKFSEAARRKIIEAGGEAISIEELMERNPKGSGVIIME |
50S ribosomal protein L19e | BS | 150 | Thermococcus Kodakarensis | MIMLKTQRRIAAELLKCGENRIWIDPERIEDVAAAITREDIKRLIHDGVIKKKPIKGQSRARARAFQEARKKGRHRGPGSKKGKKTARMGKKEVWMMTIRALRKELRKLKAEGKLDAHTYRRLYIRAKGGQFKNKRQLYMFMQEHGILKE |
50S ribosomal protein L18Ae | BT | 77 | Thermococcus Kodakarensis | MEVKVFRVKGTFERLGKKQPFTKEYRALKEEHVRELVYSDIGSKHRVPRTKIWIESIEEIKPEEAEDPVVRRLSLEL |
50S ribosomal protein L21e | BU | 98 | Thermococcus Kodakarensis | MVKKAHSFRRKTRGKLSKHPRRRGLPPLTRFLQEFEVGQKVHIVIEPSYHKGMPDPRFHGRTGTVVGKRGDAYIVQITDGGKVKTFFIHPVHLRPQKG |
50S ribosomal protein L22 | BV | 156 | Thermococcus Kodakarensis | MSRGRFSYSFQNFDPERMARASGRDLRISPKHSVELLREIRGMMLNDALRYLDDVIAKKRPVPMKRFNDSQGHKPGKGFGPGRYPVKVAKAVKKILLNAKNNAEQKGLDVDRLKIIHAAAHRGPVLRGYIPRAFGRATPFNEQTTHIEIVVEEIRR |
50S ribosomal protein L23 | BW | 86 | Thermococcus Kodakarensis | MDPYKVIIRPLVTEKAVSLIERENKLTFIVDRRATKQDIKRAVEEMFNVKVAKVNTLVTMKGEKKAYVKLKPEYDASEIAARLGLF |
50S ribosomal protein L24 | BX | 121 | Thermococcus Kodakarensis | MKLDMKQPRKQRKFLYNAPLHLRGKIMSAPLSKELREKYGVRNLPIRVGDKVKVMRGDFKGVEGKVVEVDLRRYRIHVEGVTHKKTDGTEVFYPLHPSNVMIVELNLEDEKREKIIERRAA |
50S ribosomal protein L24e | BY | 67 | Thermococcus Kodakarensis | MARWNVCSYCGREFEPGTGKMFVRNDGRVLFFCSSKCEKYYFMGRNPRKLKWTKAFQEARLQRAKRK |
30S ribosomal protein S4 | AE | 180 | Thermococcus Kodakarensis | MGDPKRQRKKYETPSHPWIKERLDRERVLKRNYALKNKKELWRHETQLKEFRRRARRLLAARGKQAEIERQQLLQRLYRLGLLPADAVLDDVLSLTVEDVLERRLQTIVYRKGLARTMKQARQLIVHGHIEVNGQVIRSPGYLVLREEEDTITYAKGSPFAKEGHPERMVIEQAKQGGEA |
50S ribosomal protein L29 | BZ | 66 | Thermococcus Kodakarensis | MKPSEIREMSIEEIDKKIRELRLELAKERGVLTMGASMENPMVIRNLRRDIARLLTIKREKLREKR |
30S ribosomal protein S4e | AF | 243 | Thermococcus Kodakarensis | MARKGPKRHLKRLAAPTSWYIHRKAYKWAVRPSPGPHSMKTSIPLIYIVRDYLGYAKTAREARKILNEGKILVDGRVRKDYKFPVGIMDVVSIPETGEHYRVLPNRIGKLILHPISEEEAKLKPFRINNKRMVKGAKVQLNLHDGSNHLVSLAEKDAYKTSYTVIMQVPERQIVKVLPFEVGAYVFVTQGKNVARKGKIVEVRQFPMGWPDVVTIEDENGELFDTLKEYAFVIGKDKPEISLP |
30S ribosomal protein S5 | AG | 235 | Thermococcus Kodakarensis | MSDPREIAQRVLEEWEPKTKLGRLVKEGQITDIHEIFRKGYQIKEPEIVDVLLPEVNLRENQEVLDIALTVRMTDSGRRIRFRVLAAVGNRDGYVGLGIGHGREVGIAIRKAINYAKMNIIEIKRGCGSWECRCRRPHSIPFAVEGKEGSVRVKLMPGPRGLGLVIGDVGKKILTLAGVQDVWSQTLGETRTTVNFAKAVFNALYNTNRVAIKPEDIERYGIVVGRAMPTTFEVE |
30S ribosomal protein S6e | AH | 125 | Thermococcus Kodakarensis | MATFKLVISNPKNGVAKQVEISGPEADKLIGRRIGEEIPASELGLNLSEIFGEEIPADAKLKITGGTDKDGFPMRPDVHGPRRVKILLSRGPGFRPRERGERRKKTVHGNTISPNIVQVNMKIVF |
30S ribosomal protein S7 | AI | 215 | Thermococcus Kodakarensis | MAKPLTERFFIPKEVKVMGRWSVEDVTVEDPSLKPYINLDARILPHSHGRYAKKPFGKANVHIVERLINKVMRSGASHYKAGGHFMRREHRSIMSKKMKAYEVVKEAFMIIERRTKQNPIQVLVKAIENSAPREDTTTIAFGGIRYHMSVDVSPLRRLDIALKNIALGASIKCYRNKTTYAQALAEEIIAAANKDPKSFAYSKKEEIERIAQSSR |
Method: ELECTRON MICROSCOPY
Deposited Date: 2019-08-15 Deposition Author(s): Matzov, D. , Meier, J.L. , Santangelo, T. , Sas-Chen, A. , Schwartz, S. , Shalev-Benami, M. , Thomas, J.M.