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5JBH

Cryo-em structure of a full archaeal ribosomal translation initiation complex in the p-in conformation

PDB DOI: 10.2210/pdb5jbh/pdb

Classification: TRANSCRIPTION
Organism(s): Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct

Deposited: 2016-04-13
Deposition Author(s): Coureux, P.-D. , Mechulam, Y. , Schmitt, E.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 5.34 Å

5jbh
Literature

Cryo-em structure of a full archaeal ribosomal translation initiation complex in the p-in conformation

Coureux, P.-D. , Mechulam, Y. , Schmitt, E.

Primary Citation of Related Structures: 5JBH


Nucleic Acids / Hybrid
Molecule Chains Sequence Length Organism Sequence
16S ribosomal RNA 2 1518 NA GUACUCCCUUUAAUUCCGGUUGAUCCUGCCGGAGGCCACUGCUAUGGGGGUCCGACUAAGCCAUGCGAGUCAAGGGGGCGUCCCUUCUGGGACGCCACCGGCGGACGGCUCAGUAACACGUCGGUAACCUACCCUCGGGAGGGGGAUAACCCCGGGAAACUGGGGCUAAUCCCCCAUAGGCCUGGGGUACUGGAAGGUCCCCAGGCCGAAAGGGAGCCGUAAGGCCCGCCCGAGGAUGCGGCGGCGGCCGAUUAGGUAGUUGGUGGGGUAACGGCCCACCAAGCCGAAGAUCGGUACGGGCCGUGAGAGCGGGAGCCCGGAGAUGGACACUGAGACACGGGUCCAGGCCCUACGGGGCGCAGCAGGCGCGAAACCUCCGCAAUGCGGGAAACCGCGACGGGGGGACCCCCAGUGCCGUGCCUCUGGCACGGCUUUUCCGGAGUGUAAAAAGCUCCGGGAAUAAGGGCUGGGCAAGGCCGGUGGCAGCCGCCGCGGUAAUACCGGCGGCCCGAGUGGUGGCCACUAUUAUUGGGCCUAAAGCGGCCGUAGCCGGGCCCGUAAGUCCCUGGCGAAAUCCCACGGCUCAACCGUGGGGCUCGCUGGGGAUACUGCGGGCCUUGGGACCGGGAGAGGCCGGGGGUACCCCCGGGGUAGGGGUGAAAUCCUAUAAUCCCGGGGGGACCGCCAGUGGCGAAGGCGCCCGGCUGGAACGGGUCCGACGGUGAGCGCGGAAGGCCAGGGGAGCGAACCGGAUUAGAUACCCGGGUAGUCCUGGCUGUAAAGGAUGCGGGCUAGGUGUCGGGCGAGCUUCGAGCUCGCCCGGUGCCGUAGGGAAGCCGUUAAGCCCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUUAAAGGAAUUGGCGGGGGAGCACUACAAGGGGUGGAGCGUGCGGUUUAAUUGGAUUCAACGCCGGGAACCUCACCGGGGGCGACGGCAGGAUGAAGGCCAGGCUGAAGGUCUUGCCGGACGCGCCGAGAGGAGGUGCAUGGCCGCCGUCAGCUCGUACCGUGAGGCGUCCACUUAAGUGUGGUAACGAGCGAGACCCGCGCCCCCAGUUGCCAGUCCCUCCCGCUCGGGAGGGAGGCACUCUGGGGGGACUGCCGGCGAUAAGCCGGAGGAAGGGGCGGGCGACGGUAGGUCAGUAUGCCCCGAAACCCCCGGGCUACACGCGCGCUACAAUGGGCGGGACAAUGGGACCCGACCUCGAAAGGGGAAGGGAAUCCCCUAAACCCGCCCUCAGUUCGGAUCGCGGGCUGCAACUCGCCCGCGUGAAGCUGGAAUCCCUAGUACCCGCGUGUCAUCAUCGCGCGGCGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUCACUCCACCCGAGCGGAGUCCGGGUGAGGCCUGAUCUCCUUCGGGAGGUCAGGUCGAGCCCGGGCUCCGUGAGGGGGGAGAAGUCGUAACAAGGUAACCGUAGGGGAACCUACGGCUCGAUCACCUCCUAUCGCCGGAA
mRNA 5 26 NA AUUUGGAGGUGAUUUAAAUGCCAAAG
initiator Met-tRNA fMet from E. coli (A1U72 variant) 4 76 NA GCGGGGUGGAGCAGCCUGGUAGCUCGUCGGGCUCAUAACCCGAAGAUCGUCGGUUCAAAUCCGGCCCCCGCUACCA

Proteins
Molecule Chains Sequence Length Organism Sequence
30S ribosomal protein eS28 X 71 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MAEDEGYPAEVIEIIGRTGTTGDVTQVKVRILEGRDKGRVIRRNVRGPVRIGDILILRETEREAREIKSRR
30S ribosomal protein eS27 Y 50 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MGQKWKLYEIKDGKVIRKNKFCPRCGPGVFMADHGDRWACGKCGYTEWKK
30S ribosomal protein uS7 H 215 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MAKPLNERFFIPHEIKVMGRWSTEDVEVRDPSLKPYINLEPRLLPHTHGRHAKKHFGKANVHIVERLINKIMRSGGSHYKVAGHFMRREHRSLNSKKVKAYEVVKEAFKIIEQRTGKNPIQVLVWAIENAAPREDTTSVMFGGIRYHVAVDISPMRRLDVALRNIALGASAKCYRNKMSFAEALAEEIILAANKDPKSYAYSKKLEIERIAESSR
30S ribosomal protein uS9 K 135 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MRIIQTTGKRKTAIARAVIREGKGRVRINGKPVEIIEPEIARFTILEPLILAGEEIWNSVDIDVKVEGGGFMGQAEAARMAIARALVEWTGDMSLKEKFMKYDRTMLVGDPRRTEPHKPNRSTKGPRAKRQKSYR
30S ribosomal protein uS11 M 137 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MSEEQVNIKKKEKWGIAHIYSSFNNTIIHITDITGAETISRWSGGMVVKADRDEPSPYAAMLAARRAAEEALEKGIVGVHIRVRAPGGSKSKTPGPGAQAAIRALARAGLKIGRVEDVTPIPHDGTRPKGGRRGRRV
30S ribosomal protein uS12 N 147 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MPGKKAPNGEFAGRKLKLKRKKFRWSDIRYKRRVLRLKEKSDPLEGAPQARGIVLEKIAVEAKQPNSGMRKAVRVQLIKNGKVVTAFCPGDGAIKFIDEHDEVIIEGIGGPKGGSMGDIPGIRYKVVKVNRVSLKELVKGRKEKPRR
30S ribosomal protein uS15 Q 158 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MARMHARKRGKSGSKRPPRTAPPIWVEYTVEEIENLVVKLRKEGYSTAMIGTILRDQYGIPSVKLFKDPDNPNRNLTITRILEKHGLAPEIPEDLMFLIRRAVNLRKHLEQHPKDLHSMRGLQLIESKIRRLVKYYKRKGKLPKNWRYDPETAKLLVR
30S ribosomal protein uS17 R 113 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MMRDIGLRVQPPAEKCDDPKCPWHGNLKIHGRVFEGIVVSDKPRKTVTVERQYYFYLNKYERYELRRSKIHAHNPPCINAKVGDKVLIAETRPLSKTKHFVVVAVLERAEERR
30S ribosomal protein uS3 A 198 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MAAKRATTTRDKWKLKQWYIIYAPDFFGGVEVGLTPADDPEKVLNRVVEVTLKDVTGDFTKSHVKLYFQVYDVKGQNAYTKFKGMKLARSYIRSLVRRKTTRIDGIFNITTKDGYKLRVMAMAIAMRRIQTSQERAIRKIMQEIIYKKAEELNFKDFVLESVNGKIAAEIAKEAKKIYPLRKAEIRKIKVLEEPQVIA
30S ribosomal protein uS2 B 202 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MADEYLVPLDQYLAAGVHIGTQQKTKDMKKFIYRVRQDGLYVLDVRKTDERLKVAGKFLAKFEPQSILAVSVRLYGQKPVKKFGEVTGARAIPGRFLPGTMTNPAVKNFFEPDVLIVTDPRADHQAMREAVEIGIPIVALVDTENLLSYVDLAIPTNNKGRKALALIYWILAREILYNRGEIQSREDFKIPVEEFEMKIVRR
30S ribosomal protein uS3 Z 210 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MAIERYFIREAVREMLIDEFLEKELRRAGYGGLDIKKTPLGTKVIIFAANPGYVIGRGGRRIRELTRILEKQFGLENPQIEVEEIKNPYLNAKVQAVRLAQALERGIHFRRAAYAALRAIMNNGARGVEIRLSGKLTGERAKSIRFYQGYLAKVGNPAETLVSKGYAQALLKLGVIGVKVAIMPPGARLPDEIEIIEKPVEEEVVSNEAE
30S ribosomal protein eS24 V 99 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MEIRIKEIKENKLIGRKEIYFEIYHPGEPTPSRKDVKGKLVAMLDLNPETTVIQYIRSYFGSYISKGYAKAYDSKERMLYIEPEYILIRDGLIEKKEGE
30S ribosomal protein eS27 W 63 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MAKPIIPMPRSRFLRVKCIDCGNEQIVFSHPATKVRCLICGATLVEPTGGKGIVKAKILEVLE
30S ribosomal protein uS4 D 180 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MGDPKRQRKKYETPPHPWIKERLDRERVLMDKYELKNKKELWKHETQLKNFRRRARRLLAARGKQAEIEREQLLARLKRLGLLPEDAVLDDVLSLTIEDILERRLQTIVYKKGLARTMRQARQLIVHGHIEVNGQIIRSPSYLVLKEEEDTITYARTSPFANPQHPERMMIEKAKQGGEA
30S ribosomal protein eS4 E 243 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MARKGPKRHLKRLAAPTSWYIERKAYKWAVRPRPGPHNMRTSIPLLYIVRDYLGYAKTAREARKILNEGKFLVDGRVRKDYKFPVGIMDVVSIPETGEHYRVLPNRIGKLILHPISEDEAFIKPLRIRNKRMIKGARVQLNFHDGTNHIVSIAEKDNYFTSYTVLMKVPEREILEVLPFEKGAYVFVTQGKNVARKGRIVEIKRFPMGWPDVVTIEDEEGELFDTLKEYAFVVGTDKPKISLP
30S ribosomal protein uS5 F 236 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MSQEWKEYAKRVLDEWEPKTKLGMMVKEGQITDIHEIFRRGYQIKEPEIIDVLLPEVNARENQEVLDIALTVRMTDSGRRVRFRVLAAVGNRDGYVGLGIGHGKEVGIAIRKAINYAKLNIIEIKRGCGSWECRCRRPHSVPFAVEGKEGSVRVRLIPGPRGLGLVIGDVGKKILRLAGVQDVWSQTFGETRTTVNFAKAVFNALYNTNRVAISPEMIERYGIVVGRAMPTTFTLE
30S ribosomal protein eS6 G 125 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MATFKLVISDPKSGIAKQVEITGAETEKLIGKRIGDQIPAKELNINLNELFGKEFPEDVKLEIRGGTDKDGFPMRPDIHGPRRVRVLLSKGPGFRPKEKGERRKKTVRGNTISPEIVQVNVKLVY
30S ribosomal protein uS8 I 130 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MTLLDPLANALSHITNSERVGKREVYIKPASKLIGEVLRVMQKYGYIGEFEFIDDGRAGVYRVQLLGRINKAGAIKPRFPVKVSEFEKWEKRFLPAFEFGILIVSTSQGVMSHKEAIEKGIGGRLIAYVY
30S ribosomal protein eS8 J 127 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MAIWQGRSLKKPSGGRIVLARKKRKRELGREPSNTRVAEQDKRKIIRTYGGNRKVRLTAAAYANVFDKSGKGRKVRIIRVIENPANRQFARRNIITKGAIIETEIGKAKVTSRPGQDGVVNAILLEE
30S ribosomal protein SX C 57 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
30S ribosomal protein eL41 0 22 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MRWKWIKKRIRRLKRQRKKERG
50S ribosomal protein uL30 3 123 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MAKPSYVKFEVPKELAEKALQAVEIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVDPEEIVAHLPPLCEEKEIPYIYVPSKKELGAAAGIEVAAASVAIIEPGKARDLVEEIAMKVKELMK
aIF1 1 102 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MPEICPRCGLPKELCVCEEIAKEEQKIKIYVTKRRFGKLMTIIEGFDTSVIDLKELAKKLKDICACGGTVKDNTIELQGDHRKKVAEELVKMGFSRDSIEIR
aIF1A 6 113 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MPKKERKVEGDEVIRVPLPEGNQLFGVVEQALGAGWMDVRCEDGKIRRCRIPGKLRRRVWIRVGDLVIVQPWPVQSDKRGDIVYRYTQTQVDWLLRKGKITQEFLTGGSLLVE
aIF2-gamma 7 415 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MAWPKVQPEVNIGVVGHVDHGKTTLVQAITGIWTSKHSEELKRGMTIKLGYAETNIGVCESCKKPEAYVTEPSCKSCGSDDEPKFLRRISFIDAPGHEVLMATMLSGAALMDGAILVVAANEPFPQPQTREHFVALGIIGVKNLIIVQNKVDVVSKEEALSQYRQIKQFTKGTWAENVPIIPVSALHKINIDSLIEGIEEYIKTPYRDLSQKPVMLVIRSFDVNKPGTQFNELKGGVIGGSIIQGLFKVDQEIKVLPGLRVEKQGKVSYEPIFTKISSIRFGDEEFKEAKPGGLVAIGTYLDPSLTKADNLLGSIITLADAEVPVLWNIRIKYNLLERVVGAKEMLKVDPIRAKETLMLSVGSSTTLGIVTSVKKDEIEVELRRPVAVWSNNIRTVISRQIAGRWRMIGWGLVEI
aIF2-beta 8 139 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MSSEKEYVEMLDRLYSKLPEKGRKEGTQSLPNMIILNIGNTTIIRNFAEYCDRIRREDKICMKYLLKELAAPGNVDDKGELVIQGKFSSQVINTLMERFLKAYVECSTCKSLDTILKKEKKSWYIVCLACGAQTPVKPL
aIF2-alpha 9 266 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MIYSRSKLPSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRVDRRKGTVDVSLKKVTDDERRKKNLQWKKIQRLDKILELVSQKLKLSEKDAWEQVAWKLEAKYGDPITAIEKAVKEGEKILIDAGVPEIWVKPLLEEASKHAEERKVKMSGLITVRTNEPLGVEKIKEVISKALENIEQDYESLLNIKIYTIGAPRYRVDVVGTNPKEASEALNQIISNLIKIGKEENVDISVVKK
30S ribosomal protein uS10 L 102 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MQKARIKIASTNVRSLDEVANQIKQIAERTGVRMSGPIPLPTKRIRITTRKSPDGEGSATFDRWELRVHKRLIDIEADERAMRQIMRIRVPEDVTIEIELIS
30S ribosomal protein uS13 O 148 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MANFRHIVRVAGVDLDGNKQLRWALTAIKGIGINFATMVCRVAGLDPFMKAGYLTDEQVKKIEEILADPVAHGIPRWAVNRPKDYETGRDLHLITAKLDMAIREDIMRLRRIRAYRGIRHELGLPVRGQRTRSNFRRGQTVGVSRKKK
30S ribosomal protein uS14 P 56 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MAKADYNKRKPRKFGKGARRCIRCGQYGPIIRIQGLMLCRHCFREVAPKLGFRKYE
30S ribosomal protein eS17 S 67 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MGKIRQGFIKRVARELVNKYPNEFTTDFEHNKKKVQELTNVTSKKIRNRIAGYVTKLVRMKMEGKIL
30S ribosomal protein uS19 T 132 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MARKEFRYRGYTLEQLMNMSLEELARLFPARQRRSLKRGLTPEQKKLLRKIRLAKKGKYKKPIRTHCRDMIILPEMVGLTIYVHNGKEFVPVEIKPEMIGHYLGEFAPTRKKVEHGAPGVGATRSSMFVAVK
30S ribosomal protein eS19 U 150 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MATVYDVPGDLLVERVAQRLKEIPEIKPPEWAPFVKTGRHKERLPEQEDWWYYRVASILRRVYLDGPVGIERLRTYYGGRKNRGHAPEKFYKAGGSIIRKALQQLEAAGFVEKVPGKGRVITPKGRSFLDKIATELKKELEEIIPELKKY
Experimental Data

Method: ELECTRON MICROSCOPY

Deposited Date: 2016-04-13
Deposition Author(s): Coureux, P.-D. , Mechulam, Y. , Schmitt, E.