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FASTA Sequence PDB Format mmCIF Format
FASTA Sequence PDB Format PDB Format(gz) PDBx/mmCIF Format PDBx/mmCIF Format(gz) PDBML/XML Format Validation Full PDF Validation CIF

6SKG

Cryo-em structure of t. kodakarensis 70s ribosome in tknat10 deleted strain

PDB DOI: 10.2210/pdb6skg/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.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.65 Å

6skg
Literature

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 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
50S ribosomal protein L14e BM 83 Thermococcus Kodakarensis MPAIEVGRIAVVIAGRRAGQKVVVADIIDKNFVLVTGAGLNKVKRRRMNVKHLEPLPERVNIQRGASDEEIKAALEGAGISLE
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
50S ribosomal protein L14e BN 83 Thermococcus Kodakarensis MPAIEVGRIAVVIAGRRAGQKVVVADIIDKNFVLVTGAGLNKVKRRRMNVKHLEPLPERVNIQRGASDEEIKAALEGAGISLE
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
Ribosomal protein eL35A BF 101 Thermococcus Kodakarensis MNGTTPWPEAEGVVVVRKAVVLSYVGSHEHRDPNRVILKPLDVNDRGSAARLIGRKVVWRTPTGRKLVGKIVRTHGTRGEVKAVFKPGLPGQALGDYVEIL
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
Nucleic acid-binding protein, containing C2H2 zinc-finger BO 47 Thermococcus Kodakarensis MAVLKAIKIEDRDGEILFRCPRCGMVFRSAKAYTRHVNKAHGHLFRK
30S ribosomal protein S3Ae AD 200 Thermococcus Kodakarensis MARGNPRKRAAAAKDKWKMKEWYIVYAPDFFGSKEIGLTPADDPEKVIGRVIETTLKDLTGDFTKGHVKLYFQVYDVKGQNAYTKFKGHTLARSYIRSLVRRRTTRVDGIFNITTKDGYKLRVMGMVIAYRRIQTSQERAIRKIIQDIIYKKAEELNFADFVLQSVNGQIASEIAKEARKIYPIKRAEVRKIKVLAEPSA
Predicted exosome subunit, UPF0023 family BP 236 Thermococcus Kodakarensis MPISVDKAVIARLKTHGETFEILVDPYLARDFKEGKDVPIEEILATPYVFKDAHKGDKASEHEMEKIFGTSDPYEVAKIILRKGEVQLTAEQRRQMLEDKKRYIATVIHRHAVDPRTGYPHPVDRILRAMEEAGVHIDIFKDAEAQVPQVIKAIRPILPLKLEVKVIAVKIPGDYVGRAYGEVRKFGNIKREEWGSDGSWMFVIEIPGGVEEEFYEKLNALTKGEAITKLLERKGL
Unknown ribosomal protein BQ 34 Thermococcus Kodakarensis AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
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
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.