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5JB3

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

PDB DOI: 10.2210/pdb5jb3/pdb

Classification: TRANSLATION
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

5jb3
Literature

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

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

Primary Citation of Related Structures: 5JB3


Nucleic Acids / Hybrid
Molecule Chains Sequence Length Organism Sequence
16S ribosomal RNA 2 1519 NA GUACUCCCUUUAAUUCCGGUUGAUCCUGCCGGAGGCCACUGCUAUGGGGGUCCGACUAAGCCAUGCGAGUCAAGGGGGCGUCCCUUCUGGGACGCCACCGGCGGACGGCUCAGUAACACGUCGGUAACCUACCCUCGGGAGGGGGAUAACCCCGGGAAACUGGGGCUAAUCCCCCAUAGGCCUGGGGUACUGGAAGGUCCCCAGGCCGAAAGGGAGCCGUAAGGCUCCGCCCGAGGAUGCGGCGGCGGCCGAUUAGGUAGUUGGUGGGGUAACGGCCCACCAAGCCGAAGAUCGGUACGGGCCGUGAGAGCGGGAGCCCGGAGAUGGACACUGAGACACGGGUCCAGGCCCUACGGGGCGCAGCAGGCGCGAAACCUCCGCAAUGCGGGAAACCGCGACGGGGGGACCCCCAGUGCCGUGCCUCUGGCACGGCUUUUCCGGAGUGUAAAAAGCUCCGGGAAUAAGGGCUGGGCAAGGCCGGUGGCAGCCGCCGCGGUAAUACCGGCGGCCCGAGUGGUGGCCACUAUUAUUGGGCCUAAAGCGGCCGUAGCCGGGCCCGUAAGUCCCUGGCGAAAUCCCACGGCUCAACCGUGGGGCUCGCUGGGGAUACUGCGGGCCUUGGGACCGGGAGAGGCCGGGGGUACCCCCGGGGUAGGGGUGAAAUCCUAUAAUCCCGGGGGGACCGCCAGUGGCGAAGGCGCCCGGCUGGAACGGGUCCGACGGUGAGCGCGGAAGGCCAGGGGAGCGAACCGGAUUAGAUACCCGGGUAGUCCUGGCUGUAAAGGAUGCGGGCUAGGUGUCGGGCGAGCUUCGAGCUCGCCCGGUGCCGUAGGGAAGCCGUUAAGCCCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUUAAAGGAAUUGGCGGGGGAGCACUACAAGGGGUGGAGCGUGCGGUUUAAUUGGAUUCAACGCCGGGAACCUCACCGGGGGCGACGGCAGGAUGAAGGCCAGGCUGAAGGUCUUGCCGGACGCGCCGAGAGGAGGUGCAUGGCCGCCGUCAGCUCGUACCGUGAGGCGUCCACUUAAGUGUGGUAACGAGCGAGACCCGCGCCCCCAGUUGCCAGUCCCUCCCGCUCGGGAGGGAGGCACUCUGGGGGGACUGCCGGCGAUAAGCCGGAGGAAGGGGCGGGCGACGGUAGGUCAGUAUGCCCCGAAACCCCCGGGCUACACGCGCGCUACAAUGGGCGGGACAAUGGGACCCGACCUCGAAAGGGGAAGGGAAUCCCCUAAACCCGCCCUCAGUUCGGAUCGCGGGCUGCAACUCGCCCGCGUGAAGCUGGAAUCCCUAGUACCCGCGUGUCAUCAUCGCGCGGCGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUCACUCCACCCGAGCGGAGUCCGGGUGAGGCCUGAUCUCCUUCGGGAGGUCAGGUCGAGCCCGGGCUCCGUGAGGGGGGAGAAGUCGUAACAAGGUAACCGUAGGGGAACCUACGGCUCGAUCACCUCCUAUCGCCGGAA
initiator Met-tRNA fMet from E. coli (A1U72 variant) 4 76 NA GCGGGGUGGAGCAGCCUGGUAGCUCGUCGGGCUCAUAACCCGAAGAUCGUCGGUUCAAAUCCGGCCCCCGCUACCA
mRNA 5 26 NA AUUUGGAGGUGAUUUAAAUGCCAAAG

Proteins
Molecule Chains Sequence Length Organism Sequence
30S ribosomal protein S3 Z 210 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MAIERYFIREAVREMLIDEFLEKELRRAGYGGLDIKKTPLGTKVIIFAANPGYVIGRGGRRIRELTRILEKQFGLENPQIEVEEIKNPYLNAKVQAVRLAQALERGIHFRRAAYAALRAIMNNGARGVEIRLSGKLTGERAKSIRFYQGYLAKVGNPAETLVSKGYAQALLKLGVIGVKVAIMPPGARLPDEIEIIEKPVEEEVVSNEAE
30S ribosomal protein S4 D 180 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MGDPKRQRKKYETPPHPWIKERLDRERVLMDKYELKNKKELWKHETQLKNFRRRARRLLAARGKQAEIEREQLLARLKRLGLLPEDAVLDDVLSLTIEDILERRLQTIVYKKGLARTMRQARQLIVHGHIEVNGQIIRSPSYLVLKEEEDTITYARTSPFANPQHPERMMIEKAKQGGEA
30S ribosomal protein S4e E 243 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MARKGPKRHLKRLAAPTSWYIERKAYKWAVRPRPGPHNMRTSIPLLYIVRDYLGYAKTAREARKILNEGKFLVDGRVRKDYKFPVGIMDVVSIPETGEHYRVLPNRIGKLILHPISEDEAFIKPLRIRNKRMIKGARVQLNFHDGTNHIVSIAEKDNYFTSYTVLMKVPEREILEVLPFEKGAYVFVTQGKNVARKGRIVEIKRFPMGWPDVVTIEDEEGELFDTLKEYAFVVGTDKPKISLP
30S ribosomal protein S5 F 236 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MSQEWKEYAKRVLDEWEPKTKLGMMVKEGQITDIHEIFRRGYQIKEPEIIDVLLPEVNARENQEVLDIALTVRMTDSGRRVRFRVLAAVGNRDGYVGLGIGHGKEVGIAIRKAINYAKLNIIEIKRGCGSWECRCRRPHSVPFAVEGKEGSVRVRLIPGPRGLGLVIGDVGKKILRLAGVQDVWSQTFGETRTTVNFAKAVFNALYNTNRVAISPEMIERYGIVVGRAMPTTFTLE
30S ribosomal protein S6e G 125 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MATFKLVISDPKSGIAKQVEITGAETEKLIGKRIGDQIPAKELNINLNELFGKEFPEDVKLEIRGGTDKDGFPMRPDIHGPRRVRVLLSKGPGFRPKEKGERRKKTVRGNTISPEIVQVNVKLVY
30S ribosomal protein S8 I 130 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MTLLDPLANALSHITNSERVGKREVYIKPASKLIGEVLRVMQKYGYIGEFEFIDDGRAGVYRVQLLGRINKAGAIKPRFPVKVSEFEKWEKRFLPAFEFGILIVSTSQGVMSHKEAIEKGIGGRLIAYVY
30S ribosomal protein S8e J 127 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MAIWQGRSLKKPSGGRIVLARKKRKRELGREPSNTRVAEQDKRKIIRTYGGNRKVRLTAAAYANVFDKSGKGRKVRIIRVIENPANRQFARRNIITKGAIIETEIGKAKVTSRPGQDGVVNAILLEE
30S ribosomal protein SX C 57 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
50S ribosomal protein L7Ae 3 123 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MAKPSYVKFEVPKELAEKALQAVEIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVDPEEIVAHLPPLCEEKEIPYIYVPSKKELGAAAGIEVAAASVAIIEPGKARDLVEEIAMKVKELMK
30S ribosomal protein S10 L 102 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MQKARIKIASTNVRSLDEVANQIKQIAERTGVRMSGPIPLPTKRIRITTRKSPDGEGSATFDRWELRVHKRLIDIEADERAMRQIMRIRVPEDVTIEIELIS
30S ribosomal protein S11 M 137 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MSEEQVNIKKKEKWGIAHIYSSFNNTIIHITDITGAETISRWSGGMVVKADRDEPSPYAAMLAARRAAEEALEKGIVGVHIRVRAPGGSKSKTPGPGAQAAIRALARAGLKIGRVEDVTPIPHDGTRPKGGRRGRRV
30S ribosomal protein S13 O 148 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MANFRHIVRVAGVDLDGNKQLRWALTAIKGIGINFATMVCRVAGLDPFMKAGYLTDEQVKKIEEILADPVAHGIPRWAVNRPKDYETGRDLHLITAKLDMAIREDIMRLRRIRAYRGIRHELGLPVRGQRTRSNFRRGQTVGVSRKKK
30S ribosomal protein S14 type Z P 56 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MAKADYNKRKPRKFGKGARRCIRCGQYGPIIRIQGLMLCRHCFREVAPKLGFRKYE
30S ribosomal protein S17e S 67 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MGKIRQGFIKRVARELVNKYPNEFTTDFEHNKKKVQELTNVTSKKIRNRIAGYVTKLVRMKMEGKIL
30S ribosomal protein S19 T 132 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MARKEFRYRGYTLEQLMNMSLEELARLFPARQRRSLKRGLTPEQKKLLRKIRLAKKGKYKKPIRTHCRDMIILPEMVGLTIYVHNGKEFVPVEIKPEMIGHYLGEFAPTRKKVEHGAPGVGATRSSMFVAVK
30S ribosomal protein S19e U 150 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MATVYDVPGDLLVERVAQRLKEIPEIKPPEWAPFVKTGRHKERLPEQEDWWYYRVASILRRVYLDGPVGIERLRTYYGGRKNRGHAPEKFYKAGGSIIRKALQQLEAAGFVEKVPGKGRVITPKGRSFLDKIATELKKELEEIIPELKKY
30S ribosomal protein S28e X 71 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MAEDEGYPAEVIEIIGRTGTTGDVTQVKVRILEGRDKGRVIRRNVRGPVRIGDILILRETEREAREIKSRR
30S ribosomal protein S27ae Y 50 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MGQKWKLYEIKDGKVIRKNKFCPRCGPGVFMADHGDRWACGKCGYTEWKK
30S ribosomal protein S7 H 215 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MAKPLNERFFIPHEIKVMGRWSTEDVEVRDPSLKPYINLEPRLLPHTHGRHAKKHFGKANVHIVERLINKIMRSGGSHYKVAGHFMRREHRSLNSKKVKAYEVVKEAFKIIEQRTGKNPIQVLVWAIENAAPREDTTSVMFGGIRYHVAVDISPMRRLDVALRNIALGASAKCYRNKMSFAEALAEEIILAANKDPKSYAYSKKLEIERIAESSR
30S ribosomal protein S9 K 135 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MRIIQTTGKRKTAIARAVIREGKGRVRINGKPVEIIEPEIARFTILEPLILAGEEIWNSVDIDVKVEGGGFMGQAEAARMAIARALVEWTGDMSLKEKFMKYDRTMLVGDPRRTEPHKPNRSTKGPRAKRQKSYR
30S ribosomal protein eL41 0 22 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MRWKWIKKRIRRLKRQRKKERG
30S ribosomal protein S12 N 147 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MPGKKAPNGEFAGRKLKLKRKKFRWSDIRYKRRVLRLKEKSDPLEGAPQARGIVLEKIAVEAKQPNSGMRKAVRVQLIKNGKVVTAFCPGDGAIKFIDEHDEVIIEGIGGPKGGSMGDIPGIRYKVVKVNRVSLKELVKGRKEKPRR
Protein translation factor SUI1 homolog 1 102 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MPEICPRCGLPKELCVCEEIAKEEQKIKIYVTKRRFGKLMTIIEGFDTSVIDLKELAKKLKDICACGGTVKDNTIELQGDHRKKVAEELVKMGFSRDSIEIR
Translation initiation factor 1A 6 113 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MPKKERKVEGDEVIRVPLPEGNQLFGVVEQALGAGWMDVRCEDGKIRRCRIPGKLRRRVWIRVGDLVIVQPWPVQSDKRGDIVYRYTQTQVDWLLRKGKITQEFLTGGSLLVE
Translation initiation factor 2 subunit gamma 7 415 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MAWPKVQPEVNIGVVGHVDHGKTTLVQAITGIWTSKHSEELKRGMTIKLGYAETNIGVCESCKKPEAYVTEPSCKSCGSDDEPKFLRRISFIDAPGHEVLMATMLSGAALMDGAILVVAANEPFPQPQTREHFVALGIIGVKNLIIVQNKVDVVSKEEALSQYRQIKQFTKGTWAENVPIIPVSALHKINIDSLIEGIEEYIKTPYRDLSQKPVMLVIRSFDVNKPGTQFNELKGGVIGGSIIQGLFKVDQEIKVLPGLRVEKQGKVSYEPIFTKISSIRFGDEEFKEAKPGGLVAIGTYLDPSLTKADNLLGSIITLADAEVPVLWNIRIKYNLLERVVGAKEMLKVDPIRAKETLMLSVGSSTTLGIVTSVKKDEIEVELRRPVAVWSNNIRTVISRQIAGRWRMIGWGLVEI
Translation initiation factor 2 subunit beta 8 139 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MSSEKEYVEMLDRLYSKLPEKGRKEGTQSLPNMIILNIGNTTIIRNFAEYCDRIRREDKICMKYLLKELAAPGNVDDKGELVIQGKFSSQVINTLMERFLKAYVECSTCKSLDTILKKEKKSWYIVCLACGAQTPVKPL
Translation initiation factor 2 subunit alpha 9 266 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MIYSRSKLPSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRVDRRKGTVDVSLKKVTDDERRKKNLQWKKIQRLDKILELVSQKLKLSEKDAWEQVAWKLEAKYGDPITAIEKAVKEGEKILIDAGVPEIWVKPLLEEASKHAEERKVKMSGLITVRTNEPLGVEKIKEVISKALENIEQDYESLLNIKIYTIGAPRYRVDVVGTNPKEASEALNQIISNLIKIGKEENVDISVVKK
30S ribosomal protein S15 Q 158 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MARMHARKRGKSGSKRPPRTAPPIWVEYTVEEIENLVVKLRKEGYSTAMIGTILRDQYGIPSVKLFKDPDNPNRNLTITRILEKHGLAPEIPEDLMFLIRRAVNLRKHLEQHPKDLHSMRGLQLIESKIRRLVKYYKRKGKLPKNWRYDPETAKLLVR
30S ribosomal protein S17P R 113 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MMRDIGLRVQPPAEKCDDPKCPWHGNLKIHGRVFEGIVVSDKPRKTVTVERQYYFYLNKYERYELRRSKIHAHNPPCINAKVGDKVLIAETRPLSKTKHFVVVAVLERAEERR
30S ribosomal protein S3Ae A 198 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MAAKRATTTRDKWKLKQWYIIYAPDFFGGVEVGLTPADDPEKVLNRVVEVTLKDVTGDFTKSHVKLYFQVYDVKGQNAYTKFKGMKLARSYIRSLVRRKTTRIDGIFNITTKDGYKLRVMAMAIAMRRIQTSQERAIRKIMQEIIYKKAEELNFKDFVLESVNGKIAAEIAKEAKKIYPLRKAEIRKIKVLEEPQVIA
30S ribosomal protein S2 B 202 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MADEYLVPLDQYLAAGVHIGTQQKTKDMKKFIYRVRQDGLYVLDVRKTDERLKVAGKFLAKFEPQSILAVSVRLYGQKPVKKFGEVTGARAIPGRFLPGTMTNPAVKNFFEPDVLIVTDPRADHQAMREAVEIGIPIVALVDTENLLSYVDLAIPTNNKGRKALALIYWILAREILYNRGEIQSREDFKIPVEEFEMKIVRR
30S ribosomal protein S24e V 99 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MEIRIKEIKENKLIGRKEIYFEIYHPGEPTPSRKDVKGKLVAMLDLNPETTVIQYIRSYFGSYISKGYAKAYDSKERMLYIEPEYILIRDGLIEKKEGE
30S ribosomal protein S27e W 63 Escherichia Coli , Pyrococcus Abyssi Ge5 , Synthetic Construct MAKPIIPMPRSRFLRVKCIDCGNEQIVFSHPATKVRCLICGATLVEPTGGKGIVKAKILEVLE
Experimental Data

Method: ELECTRON MICROSCOPY

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