6SKG
Cryo-em structure of t. kodakarensis 70s ribosome in tknat10 deleted strain
PDB DOI: 10.2210/pdb6skg/pdb
Classification: RIBOSOME Organism(s): Penicillium Sp.
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.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 2.65 Å
Cryo-em structure of t. kodakarensis 70s ribosome in tknat10 deleted strain
Matzov, D. , Meier, J.L. , Santangelo, T. , Sas-Chen, A. , Schwartz, S. , Shalev-Benami, M. , Thomas, J.M.
Primary Citation of Related Structures: 6SKG
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 16S ribosomal RNA | aa | 1498 | NA | AUUCCGGUUGAUCCUGCCGGAGGCCACUGCUAUGGGGGUCCGACUAAGCCAUGCGAGUCAUGGGGCGCGCUCUGCGCGCACCGGCGGACGGCUCAGUAACACGUCGGUAACCUACCCUCGGGAGGGGGAUAACCCCGGGAAACUGGGGCUAAUCCCCCAUAGGCCUGAGGUACUGGAAGGUCCUCAGGCCGAAAGGGGCAUCUGCCCGCCCGAGGAUGGGCCGGCGGCCGAUUAGGUAGUUGGUGGGGUAACGGCCCACCAAGCCGAAGAUCGGUACGGGCCAUGAGAGUGGGAGCCCGGAGAUGGACACUGAGACACGGGUCCAGGCCCUACGGGGCGCAGCAGGCGCGAAACCUCCGCAAUGCGGGCAACCGCGACGGGGGGACCCCCAGUGCCGUGGCAUAGCCACGGCUUUUCCGGAGUGUAAAAAGCUCCGGGAAUAAGGGCUGGGCAAGGCCGGUGGCAGCCGCCGCGGUAAUACCGGCGGCCCGAGUGGUGGCCGCUAUUAUUGGGCCUAAAGCGUCCGUAGCCGGGCCCGUAAGUCCCUGGCGAAAUCCCACGGCUCAACCGUGGGGCUUGCUGGGGAUACUGCGGGCCUUGGGACCGGGAGAGGCCGGGGGUACCCCUGGGGUAGGGGUGAAAUCCUAUAAUCCCAGGGGGACCGCCAGUGGCGAAGGCGCCCGGCUGGAACGGGUCCGACGGUGAGGGACGAAGGCCAGGGGAGCGAACCGGAUUAGAUACCCGGGUAGUCCUGGCUGUAAAGGAUGCGGGCUAGGUGUCGGGCGAGCUUCGAGCUCGCCCGGUGCCGGAGGGAAGCCGUUAAGCCCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUUAAAGGAAUUGGCGGGGGAGCACUACAAGGGGUGGAGCGUGCGGUUUAAUUGGAUUCAACGCCGGGAACCUCACCGGGGGCGACGGCAGGAUGAAGGCCAGGCUGAAGGUCUUGCCGGACACGCCGAGAGGAGGUGCAUGGCCGCCGUCAGCUCGUACUGUGAGGCGUCCACUUAAGUGUGGUAACGAGCGAGACCCGCGCCCCCAGUUGCCAGUCCUCCCCGCUGGGGAGGAGGCACUCUGGGGGGACCGCCGGCGAUAAGCCGGAGGAAGGAGCGGGCGACGGUAGGUCAGUAUGCCCCGAAACCCCCGGGCUACACGCGCGCUACAAUGGGCGGGACAAUGGGAUCCGACCCCGAAAGGGGAAGGGAAUCCCCUAAACCCGCCCUCAGUUCGGAUCGCGGGCUGCAACUCGCCCGCGUGAAGCUGGAAUCCCUAGUACCCGCGUGUCAUCAUCGCGCGGCGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUCACUCCACCCGAGCGGGGUCCGGGUGAGGCCUGGUCUCCCUUCGGGGAGGCCGGGUCGAGCCUGGGCUCCGUGAGGGGGGAGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUACGGCUCGAUCACCUCCUAUCGCCGGA |
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 30S ribosomal protein S8 | AJ | 130 | Penicillium Sp. | MTLLDPLANALSHITNSERVGKKEVYIKPASKLIGEVLRVMLENGYIGEFELIDDGRAGIYRVQLIGKINKAGAIKPRFPVKARDYEKWEKRFLPAFEFGILIVSTSQGVMTHKEALEKGIGGRLIAYVY |
| 30S ribosomal protein S8e | AK | 130 | Penicillium Sp. | MAIWQGRSLKKPSGGRIILARKKRKRELGREPANTKVGEDREKRKIIRTYGGNRKVRLVEALYANVFEGGKGKKVKILNVVENPANRQYARRNIITKGAIIETEIGKAIVTSRPGQDGVVNAVLIKEENA |
| 30S ribosomal protein S9 | AL | 135 | Penicillium Sp. | MRVIQTAGKRKTAVARATIREGKGRVRINHKPVEIIEPEIARFTIMEPLILAGEEIVSRVDIDVKVEGGGFMGQAEAARVAIARALVEWTNDMNLKEKFMKYDRTMLVGDSRRTEPHKPNRSTKGPRAKRQKSYR |
| 30S ribosomal protein S10 | AM | 102 | Penicillium Sp. | MQKARIKLASTNIKALNEVTDQIKQIAERTGVRMSGPIPLPTKRIRITTRKSPDGEGSATFDRFELRVHKRLVDIEADERAMRQIMRIRVPEDVTIEIELIS |
| 30S ribosomal protein S11 | AN | 140 | Penicillium Sp. | MSEEQTTQVNIKKKEKWGVAHIYSSYNNTIIHITDLTGAETISRWSGGMVVKADRDEPSPYAAMIAARRAAEEAMEKGITGVHIKVRAPGGSKSKSPGPGAQAAIRALSRAGLRIGRVEDVTPIPHDGTRPKGGRRGRRV |
| 30S ribosomal protein S12 | AO | 147 | Penicillium Sp. | MAGKKAPYGEFAGRKLKLKRKKFRWSDIRYKRRVLRLKEKSDPLEGAPQARGIVLEKIAVEAKQPNSAMRKAVRVQLIKNGKVVTAFTPGDGAINHIDEHDEVIIEGIGGPKGGSMGDIPGIRYKVVKVNRVSLKELVKGRKEKPRR |
| 30S ribosomal protein S13 | AP | 149 | Penicillium Sp. | MTENFRHIVRVAGVDIDGHKQVRWALTGIKGIGINFATMVLRVAGIDPFMKAGYLTDEQVKKIEEILADPVAHGIPAWAVNRPKDYETGKDMHLITAKLVMAWREDVNRLRRIRAYRGIRHELGLPVRGQRTRSNFRHGTTVGVSRRKK |
| 30S ribosomal protein S15 | AQ | 151 | Penicillium Sp. | MARIHARKRGKSGSKRPPRTAPPAWVEYTAEEVEALVVKLRKEGYSTAMIGTILRDQYGIPSVKLITGKKITKILEENGLAPEIPEDLMFLIRRAVNLRKHLEQHPKDKHSRRGLQLIESKIRRLVKYYRRTGKLPAKWRYDPEQAKLLVR |
| 30S ribosomal protein S14 type Z | AR | 56 | Penicillium Sp. | MAKADYNKRKPRKFGKGARRCMRCGQYGPIIRIHGLMLCRHCFREVAPKLGFKKYE |
| 30S ribosomal protein S17 | AS | 114 | Penicillium Sp. | MREIGLRVQPPAEVCNDPKCPWHGNLKIHGRYVEGIVVSDKGKKTVVVERQYYHYLKKYERYELRKSKVHAHNPECINAKVGDKVLIAETRPISKTKSWVVVAVLQRAERAEEV |
| 30S ribosomal protein S2 | AB | 201 | Penicillium Sp. | MEEYLVPLDQYLAAGVHIGTQQKTKDMKKFIYRVRQDGLYVLDVRKTDERLRVAGKFLAKFDPESILAVSVRLYGQRPVKKFGEVTGAKAIPGRFLPGTMTNPQVKNFIEPDVLIVTDPRADHQALKEAVEIGIPIVALVDTENFLSYVDIAIPTNNKGRKALALIYWILAREVLYNRKEIESREDFKIPVEDFEMRIIRT |
| 30S ribosomal protein S17e | AT | 67 | Penicillium Sp. | MGNIKQTFIKRTARELFDRYPDKFTRDFEHNKKMVAELTNVTSKTIRNRIAGYITRLVRMKEEGKIL |
| 50S ribosomal protein L14e | BM | 83 | Penicillium Sp. | MPAIEVGRIAVVIAGRRAGQKVVVADIIDKNFVLVTGAGLNKVKRRRMNVKHLEPLPERVNIQRGASDEEIKAALEGAGISLE |
| 30S ribosomal protein S19 | AU | 133 | Penicillium Sp. | MARKKEFRYRGYTLDELLNMSLEEFAKLLPSRQRRSLKRGLSPEQKKLLRKIRLAKKGKYNKPIRTHSRDMIVLPEMVGMTIHVYNGKEFVPVEIKEEMIGHYLGEFAMTRKVVQHGSPGVGATRSSMFVAVK |
| 30S ribosomal protein S19e | AV | 150 | Penicillium Sp. | MATVYDVPGDLLVERVAKALKEVPEIKPPEWAPFVKTGRHKERLPEQEDWWYYRVASVFRKVYIDGPVGIERLRTWYGGRKNRGHAPEHFYKAGGSIIRKALQQLEAAGFVQKVPGEGRIVTPKGQSFLDKIATELKKELEEQIPELKKY |
| 30S ribosomal protein S24e | AW | 98 | Penicillium Sp. | MEIKVTEIRENKLLGRKEIYFDVLHEGEPTPSREAVKGKLVAMLDLDPNTTVIQYIRSYFGSNVSKGYAKAYETRERMLYIEPEYILVRDGLVQKQEE |
| 50S ribosomal protein L14e | BN | 83 | Penicillium Sp. | MPAIEVGRIAVVIAGRRAGQKVVVADIIDKNFVLVTGAGLNKVKRRRMNVKHLEPLPERVNIQRGASDEEIKAALEGAGISLE |
| 30S ribosomal protein S27e | AX | 65 | Penicillium Sp. | MALPKNLIPMPRSRFLRVKCIDCGNEQIVFSHPATPVRCLVCGATLVEPTGGKGIIKAKVLEVEE |
| 30S ribosomal protein S28e | AY | 70 | Penicillium Sp. | MSDEGYPAEVIEIVGRTGVTGGVTQVKVRILEGRDKGRVIRRNVKGPVRVGDIVILRETEREAREIRRRR |
| Predicted zinc-ribbon RNA-binding protein involved in translation | AZ | 62 | Penicillium Sp. | MFAVEMKFEVPVCTSCGKEITPREHATHFVCPNCGEAIIWRCESCRVLSVPYKCPKCGWEGP |
| 50S ribosomal protein L30 | BA | 155 | Penicillium Sp. | MAKLALIRLRSGIRARGEVRDTLAMLRLHRINHLVIVDDTPSYRGMIQKVKDYITWGEIDKETLAKLLRKRGRLIGNKPITDEYVKEKLGMTIEEFAEKVVNGEMKLRDLPNIKPVFRLHPPRGGLKGSKKRSFKEGGALGYRGEKINELIERML |
| 50S ribosomal protein L30e | BB | 102 | Penicillium Sp. | MVDFAFELRKVQDTGKIVMGAKKSIHLAKVGGAKLIIVARNARPDIKEDIYYYAKLSGIPVYEFEGTSVELGTLLGRPHTVSALAVIDPGESKILALAGGKE |
| 50S ribosomal protein L31e | BC | 90 | Penicillium Sp. | MPIKPGEEVIFVVPINKIKKRVPRWKRAPRAARFVREWIARHAKADEVIIGTDVNEKIWERGAEKPPGKLRVKVVVEESEGKRIARVSLA |
| 30S ribosomal protein S3 | AC | 209 | Penicillium Sp. | MAIERYFIKEGVKEMLIDEFLEKELRRAGYGGLDIKKTPLGTKVTIFAANPGYVIGRGGRRIRELTRILEKQFGLENPQIEVEEIKNPYLNAKVQAVRLAQALERGIHFRRAAYSAIRAIMRNGARGVEIRLSGKLTGERAKSVRFYQGYLAKVGNPAETLVSRGYAQAQLKLGVIGVKVSIMPPDAKLPDEIEIKEIVEEEVSANEAQ |
| 50S ribosomal protein L32e | BD | 125 | Penicillium Sp. | MNEKARLLRIRAKLKRKKPRFLRQEWWRYPKFKNDPKWRRPKGIDSKMRLKKKGKPRSPSIGWSSPKAVRGLHPSGYEEVLVHNVKELEAIDPTRQAARIAGTVGARKREMILARAKELGVKVLN |
| 50S ribosomal protein L34e | BE | 90 | Penicillium Sp. | MKPMYRSRSWRRKYVRTPGGRTVIHFERRKPKVAHCAMCGRPLNGVPRGRPSELRKLPKTKKRPERPYPNLCPSCMRKVMKAQVRASITA |
| Ribosomal protein eL35A | BF | 101 | Penicillium Sp. | MNGTTPWPEAEGVVVVRKAVVLSYVGSHEHRDPNRVILKPLDVNDRGSAARLIGRKVVWRTPTGRKLVGKIVRTHGTRGEVKAVFKPGLPGQALGDYVEIL |
| 50S ribosomal protein L37Ae | BG | 86 | Penicillium Sp. | MGRTTKVGSAGRFGPRYGLKIRRRVAAVEARMKQKHVCPVCGRKAVRRISTGIWQCQKCGATFAGGAYLPTTPAGKVAKRVTASKA |
| 50S ribosomal protein L37e | BH | 63 | Penicillium Sp. | MGAGTAPKGKRNRTPTHIRCRRCGRRAFNVKKGYCAACGFGRSRRMRKYSWSHKWRKKRNLSY |
| 50S ribosomal protein L39e | BI | 51 | Penicillium Sp. | MARNKPFAKKLRLAKAAKQNRRVPVWVIVKTNRKVITHPKRRHWRRTKLKE |
| 50S ribosomal protein L40e | BJ | 51 | Penicillium Sp. | MARFPEAEARIFRKLVCMRCGATNPWGAKKCRKCGYKGLRPKAREPRGGGR |
| LSU ribosomal protein L41E | BK | 37 | Penicillium Sp. | MKRRPRKWKKKGRMRWKWIKKRIRRLKRQRRKERGLI |
| 50S ribosomal protein L44e | BL | 94 | Penicillium Sp. | MKYPKQIRTYCPFCKRHTIHKVEKVKKRPRSELSAGQRRFRRKLKGYTGFPRPNPAGREKPVKKLDLRFRCTVCGKAHTRGQGFRVKKFELVEV |
| Nucleic acid-binding protein, containing C2H2 zinc-finger | BO | 47 | Penicillium Sp. | MAVLKAIKIEDRDGEILFRCPRCGMVFRSAKAYTRHVNKAHGHLFRK |
| 30S ribosomal protein S3Ae | AD | 200 | Penicillium Sp. | MARGNPRKRAAAAKDKWKMKEWYIVYAPDFFGSKEIGLTPADDPEKVIGRVIETTLKDLTGDFTKGHVKLYFQVYDVKGQNAYTKFKGHTLARSYIRSLVRRRTTRVDGIFNITTKDGYKLRVMGMVIAYRRIQTSQERAIRKIIQDIIYKKAEELNFADFVLQSVNGQIASEIAKEARKIYPIKRAEVRKIKVLAEPSA |
| Predicted exosome subunit, UPF0023 family | BP | 236 | Penicillium Sp. | MPISVDKAVIARLKTHGETFEILVDPYLARDFKEGKDVPIEEILATPYVFKDAHKGDKASEHEMEKIFGTSDPYEVAKIILRKGEVQLTAEQRRQMLEDKKRYIATVIHRHAVDPRTGYPHPVDRILRAMEEAGVHIDIFKDAEAQVPQVIKAIRPILPLKLEVKVIAVKIPGDYVGRAYGEVRKFGNIKREEWGSDGSWMFVIEIPGGVEEEFYEKLNALTKGEAITKLLERKGL |
| Unknown ribosomal protein | BQ | 34 | Penicillium Sp. | AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
| 50S ribosomal protein L18e | BR | 121 | Penicillium Sp. | MVKRTGPTDINLRRLIRTLRKKSNEEGVKIWKDIAWRLERPRRQRAEVNISKINRYTKEGDVVIVPGSVLGAGRLEHKVVVAAWKFSEAARRKIIEAGGEAISIEELMERNPKGSGVIIME |
| 50S ribosomal protein L19e | BS | 150 | Penicillium Sp. | MIMLKTQRRIAAELLKCGENRIWIDPERIEDVAAAITREDIKRLIHDGVIKKKPIKGQSRARARAFQEARKKGRHRGPGSKKGKKTARMGKKEVWMMTIRALRKELRKLKAEGKLDAHTYRRLYIRAKGGQFKNKRQLYMFMQEHGILKE |
| 50S ribosomal protein L18Ae | BT | 77 | Penicillium Sp. | MEVKVFRVKGTFERLGKKQPFTKEYRALKEEHVRELVYSDIGSKHRVPRTKIWIESIEEIKPEEAEDPVVRRLSLEL |
| 50S ribosomal protein L21e | BU | 98 | Penicillium Sp. | MVKKAHSFRRKTRGKLSKHPRRRGLPPLTRFLQEFEVGQKVHIVIEPSYHKGMPDPRFHGRTGTVVGKRGDAYIVQITDGGKVKTFFIHPVHLRPQKG |
| 50S ribosomal protein L22 | BV | 156 | Penicillium Sp. | MSRGRFSYSFQNFDPERMARASGRDLRISPKHSVELLREIRGMMLNDALRYLDDVIAKKRPVPMKRFNDSQGHKPGKGFGPGRYPVKVAKAVKKILLNAKNNAEQKGLDVDRLKIIHAAAHRGPVLRGYIPRAFGRATPFNEQTTHIEIVVEEIRR |
| 50S ribosomal protein L23 | BW | 86 | Penicillium Sp. | MDPYKVIIRPLVTEKAVSLIERENKLTFIVDRRATKQDIKRAVEEMFNVKVAKVNTLVTMKGEKKAYVKLKPEYDASEIAARLGLF |
| 50S ribosomal protein L24 | BX | 121 | Penicillium Sp. | MKLDMKQPRKQRKFLYNAPLHLRGKIMSAPLSKELREKYGVRNLPIRVGDKVKVMRGDFKGVEGKVVEVDLRRYRIHVEGVTHKKTDGTEVFYPLHPSNVMIVELNLEDEKREKIIERRAA |
| 50S ribosomal protein L24e | BY | 67 | Penicillium Sp. | MARWNVCSYCGREFEPGTGKMFVRNDGRVLFFCSSKCEKYYFMGRNPRKLKWTKAFQEARLQRAKRK |
| 30S ribosomal protein S4 | AE | 180 | Penicillium Sp. | MGDPKRQRKKYETPSHPWIKERLDRERVLKRNYALKNKKELWRHETQLKEFRRRARRLLAARGKQAEIERQQLLQRLYRLGLLPADAVLDDVLSLTVEDVLERRLQTIVYRKGLARTMKQARQLIVHGHIEVNGQVIRSPGYLVLREEEDTITYAKGSPFAKEGHPERMVIEQAKQGGEA |
| 50S ribosomal protein L29 | BZ | 66 | Penicillium Sp. | MKPSEIREMSIEEIDKKIRELRLELAKERGVLTMGASMENPMVIRNLRRDIARLLTIKREKLREKR |
| 30S ribosomal protein S4e | AF | 243 | Penicillium Sp. | MARKGPKRHLKRLAAPTSWYIHRKAYKWAVRPSPGPHSMKTSIPLIYIVRDYLGYAKTAREARKILNEGKILVDGRVRKDYKFPVGIMDVVSIPETGEHYRVLPNRIGKLILHPISEEEAKLKPFRINNKRMVKGAKVQLNLHDGSNHLVSLAEKDAYKTSYTVIMQVPERQIVKVLPFEVGAYVFVTQGKNVARKGKIVEVRQFPMGWPDVVTIEDENGELFDTLKEYAFVIGKDKPEISLP |
| 30S ribosomal protein S5 | AG | 235 | Penicillium Sp. | MSDPREIAQRVLEEWEPKTKLGRLVKEGQITDIHEIFRKGYQIKEPEIVDVLLPEVNLRENQEVLDIALTVRMTDSGRRIRFRVLAAVGNRDGYVGLGIGHGREVGIAIRKAINYAKMNIIEIKRGCGSWECRCRRPHSIPFAVEGKEGSVRVKLMPGPRGLGLVIGDVGKKILTLAGVQDVWSQTLGETRTTVNFAKAVFNALYNTNRVAIKPEDIERYGIVVGRAMPTTFEVE |
| 30S ribosomal protein S6e | AH | 125 | Penicillium Sp. | MATFKLVISNPKNGVAKQVEISGPEADKLIGRRIGEEIPASELGLNLSEIFGEEIPADAKLKITGGTDKDGFPMRPDVHGPRRVKILLSRGPGFRPRERGERRKKTVHGNTISPNIVQVNMKIVF |
| 30S ribosomal protein S7 | AI | 215 | Penicillium Sp. | MAKPLTERFFIPKEVKVMGRWSVEDVTVEDPSLKPYINLDARILPHSHGRYAKKPFGKANVHIVERLINKVMRSGASHYKAGGHFMRREHRSIMSKKMKAYEVVKEAFMIIERRTKQNPIQVLVKAIENSAPREDTTTIAFGGIRYHMSVDVSPLRRLDIALKNIALGASIKCYRNKTTYAQALAEEIIAAANKDPKSFAYSKKEEIERIAQSSR |
Experimental Data
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.