6SWD
Ic2 body model of cryo-em structure of a full archaeal ribosomal translation initiation complex devoid of aif1 in p. abyssi
PDB DOI: 10.2210/pdb6swd/pdb
Classification: RIBOSOME Organism(s): Pyrococcus Abyssi (Strain Ge5 / Orsay) , Pyrococcus Abyssi Ge5 , Synthetic Construct
Deposited: 2019-09-20 Deposition Author(s): Coureux, P.-D. , Mechulam, Y. , Schmitt, E.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 3.2 Å
Ic2 body model of cryo-em structure of a full archaeal ribosomal translation initiation complex devoid of aif1 in p. abyssi
Coureux, P.-D. , Mechulam, Y. , Schmitt, E.
Primary Citation of Related Structures: 6SWD
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 16S ribosomal RNA | 2 | 1044 | NA | AUUCNGGUUGAUCCUGCCGGAGGCCACUGCUAUGGGGGUCNGACUAAGCCAUGCGAGUCAAGGGGGCGUCCCUUCUGGGACGCCACCGGCGGACGGCUCAGUAACACGUCGGUAACCUACCCUCGGGAGGGGGAUAACCCCGGGAAACUGGGGCUAAUCCCCCAUAGGCCUGGGGUACUGGAAGGUCCCCAGGCCGAAAGGGAGCCGUAAGGCUCCGCCCGAGGAUGGGCCGGCGGCCGAUUAGGUAGUUGGUGGGGUAACGGCCCACCAAGCNGAAGAUCGGUACGGGCNGUGAGAGCGGGAGCCNGGAGAUGGACACUGAGACACGGGUCCAGGCCCUACGGGGCGCAGCAGGCGCGAAACCUCNGCAAUGCGGGAAACNGCGACGGGGGGACCCCCAGUGCCGUGCCUCUGGCACGGCUUUUCCGGAGUGUAAAAAGCUCCGGGAAUAAGGGCUGGGCAAGGCNGGUGGCAGCCGCCGCGGUAAUACCGGCGGCCNGAGUGGUGGCCACUAUUAUUGGGCCUAAAGCGGCNGUAGCCGGGCCCGUAAGUCCCUGGCGAAAUCCCACGGCUCAACNGUGGGGCUCGCUGGGGAUACUGCGGGCCUUGGGACNGGGAGAGGCNGGGGGUACCCCNGGGGUAGGGGUGAAAUCCUAUAAUCCCGGGGGGACCGCCAGUGGCGAAGGCGCCNGGCUGGAACGGGUCNGACGGUGAGGGCNGAAGGCCAGGGGAGCGAACNGGAUUAGAUACCCGGGUAGUCCUGGCUGUAAAGGAUGCGGGCUAGGUGUCGGGCGAGCUUCGAGCUCGCCCGGUGCNGUAGGGAAGCNGUUAAGCCNGCNGCCUGGGGAGUACGGCNGCAAGGCUGAAACUUAAAGGAAUUGGCGGGGGAGCCUGCUCCUUGCACACACCGCCXGUCACUCCACCCGAGCGGGGCCUAGGUGAGGCCCGAUCUCCUUCGGGAGGUCGGGUCGAGCCUAGGCUCCGUGAGGGGGGAGAAGUCGUAACAAGGUAGCNGUAGGGGAACCUACGGCUCGAUCACCUCCU |
| mRNA | 5 | 20 | NA | UGGAGGUGAUUUAAAUGCCA |
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 30S ribosomal protein S8e | J | 127 | Pyrococcus Abyssi (Strain Ge5 / Orsay) , Pyrococcus Abyssi Ge5 , Synthetic Construct | MAIWQGRSLRKPSGGRIVLARKKRKRELGREPSNTRVAEQDKRKIIRTYGGNKKVRLTAAAYANVFDKSGKGRKVRIIRVIENPANRQFARRNIITKGAIIETEIGKAKVTSRPGQDGVVNAILLEE |
| 30S ribosomal protein S11 | M | 137 | Pyrococcus Abyssi (Strain Ge5 / Orsay) , Pyrococcus Abyssi Ge5 , Synthetic Construct | MSEEQVNIKKKEKWGIAHIYSSYNNTIIHITDITGAETISRWSGGMVVKADRDEPSPYAAMLAARRAAEEALEKGIVGVHIRVRAPGGSKSKTPGPGAQAAIRALARAGLKIGRVEDVTPIPHDGTRPKGGRRGRRV |
| 30S ribosomal protein S12 | N | 147 | Pyrococcus Abyssi (Strain Ge5 / Orsay) , Pyrococcus Abyssi Ge5 , Synthetic Construct | MPGKKAPNGEFAGRKLKLKRKKFRWSDIRYKRRVLRLKEKSDPLEGAPQARGIVLEKIAVEAKQPNSGMRKAVRVQLIKNGKVVTAFCPGDGAIKFIDEHDEVIIEGIGGPKGGSMGDIPGIRYKVVKVNRVSLKELVKGRKEKPRR |
| 30S ribosomal protein S15 | Q | 158 | Pyrococcus Abyssi (Strain Ge5 / Orsay) , Pyrococcus Abyssi Ge5 , Synthetic Construct | MARMHARKRGKSGSKRPPRTAPPIWLEYTVEDIENLVVKLRKEGYSTAMIGTILRDQYGIPTVKLFRDPDNPNRKLTITRILEKHGLAPEIPEDLMFLIKRAVNLRKHLEQHPKDLHSMRGLQLIESKIRRLVKYYKRKGKLPKDWRYDPEQAKLLVR |
| 30S ribosomal protein S17 | R | 113 | Pyrococcus Abyssi (Strain Ge5 / Orsay) , Pyrococcus Abyssi Ge5 , Synthetic Construct | MVRDIGLRIQPPAEKCDDPKCPWHGHLKIHGRVFEGIVVSDKPRKTVTVERQYYHYLKKYERYELRRSRIHAHNPPCINAKVGDRVLIAETRPLSKTKHFVVVAVLERAEERR |
| 30S ribosomal protein S24e | V | 99 | Pyrococcus Abyssi (Strain Ge5 / Orsay) , Pyrococcus Abyssi Ge5 , Synthetic Construct | MEIKITEVKENKLIGRKEIYFEIYHPGEPTPSRKDVKGKLVAMLDLNPETTVIQYIRSYFGSYKSKGYAKYYYDKDRMLYIEPEYILIRDGIIEKKEGE |
| 30S ribosomal protein S27e | W | 65 | Pyrococcus Abyssi (Strain Ge5 / Orsay) , Pyrococcus Abyssi Ge5 , Synthetic Construct | MALPRNVIPMPRSRFLRVKCIDCGNEQIVFSHPATRVRCNVCGATLVEPTGGKGIIRAKILEVLE |
| 30S ribosomal protein aL41 | 0 | 36 | Pyrococcus Abyssi (Strain Ge5 / Orsay) , Pyrococcus Abyssi Ge5 , Synthetic Construct | MKRRPRKWKKKGRMRWKWIKKRIRRLKRQRKKERGL |
| Translation initiation factor 1A | 6 | 113 | Pyrococcus Abyssi (Strain Ge5 / Orsay) , Pyrococcus Abyssi Ge5 , Synthetic Construct | MPKKERKVEGDEVIRVPLPEGNQLFGVVEQALGAGWMDVRCEDGKIRRCRIPGKLRRRVWIRVGDLVIVQPWPVQSDKRGDIVYRYTQTQVDWLLRKGKITQEFLTGGSLLVE |
| 30S ribosomal protein S3Ae | A | 199 | Pyrococcus Abyssi (Strain Ge5 / Orsay) , Pyrococcus Abyssi Ge5 , Synthetic Construct | MAAKRRVSAAKDKWKLKQWYVIYAPDFFGGVEVGLTPADDPEKVLNRVVEVTLKDITGDFLKGHVKLYFQVYDVKGQNAYTKFKGMKLARSYIRSLVRRRTTRIDGIFNITTKDGYKLRVMAMVIAARRIQTSQERAIRKIMQEIIYKKAEELNFKDFVLEAVNGKIAAEIAKEAKKIYPLKKAEIRKIKVLGEPEVAA |
| 30S ribosomal protein S2 | B | 202 | Pyrococcus Abyssi (Strain Ge5 / Orsay) , Pyrococcus Abyssi Ge5 , Synthetic Construct | MADEYLVPLDQYLAAGVHIGTQQKTKDMKKFIYRVRQDGLYVLDVRKTDERLKVAGKFLARFDPQSILAVSVRLYGQKPVKKFGEVTGARAIPGRFLPGTMTNPAVKNFFEPDVIIITDPRADHQAMKEAIEIGIPIVALVDTENLLSYVDLAIPTNNKGRKALALIYWILAREILYNRGEISSREEFKIPVEEFEMKIVRR |
| Zn-ribbon RNA-binding protein involved in translation | C | 63 | Pyrococcus Abyssi (Strain Ge5 / Orsay) , Pyrococcus Abyssi Ge5 , Synthetic Construct | MAENVELKFEIPVCTSCGREITPREHATHFVCPNCGEAIIWRCETCRLLAKPYKCPKCGWEGP |
| 30S ribosomal protein S4 | D | 180 | Pyrococcus Abyssi (Strain Ge5 / Orsay) , Pyrococcus Abyssi Ge5 , Synthetic Construct | MGDPKRQRKKYETPPHPWIKERLDRERVLMDKYELKNKKELWKHETQLKNFRRRARRLLAARGKQAEIEREQLLARLKRLGLLPEDAVLDDVLSLTIEDILERRLQTIVYKKGLARTMRQARQLIVHGHIEVNGQIIRSPSYLVLKEEEDTITYARTSPFANPQHPERMMIEKAKQGGEA |
| 30S ribosomal protein S4e | E | 243 | Pyrococcus Abyssi (Strain Ge5 / Orsay) , Pyrococcus Abyssi Ge5 , Synthetic Construct | MARKGPKRHLKRLAAPTSWYIERKAYKWAVRPRPGPHNMRTSIPLLYIVRDYLGYAKTAREARKILNEGKFLVDGRVRKDYKFPVGIMDVVSIPETGEHYRVLPNRIGKLILHPISEEEANIKPLRIRNKRMVKGAKIQLNFHDGTNHLIPLSEKDNYFTSYTVLMKVPEREILEVLPFEKGAYVFVTQGKNVARKGRIVEIKKFPMGWPDVVTIEDEEGELFDTLKEYAFVVGRDKPRISLP |
| 30S ribosomal protein S5 | F | 236 | Pyrococcus Abyssi (Strain Ge5 / Orsay) , Pyrococcus Abyssi Ge5 , Synthetic Construct | MSQEWKEYAKRVLDEWQPKTKLGMLVKEGQITDIHEIFRKGYQIKEPEIIDVLLPEVNARENQEILDIALTVRMTDSGRRVRFRVLAAVGNRDGYVGLGIGHGREVGIAIRKAINYAKLNIIEIKRGCGSWECRCRRPHSVPFTVEGKEGSVRVKLIPGPRGLGLVIGDVGKKILRLAGIQDVWSQTLGETRTTVNFAKAVFNALYNTNKVVVTPEMIERYGIVVGRAMPASFTLE |
| 30S ribosomal protein S6e | G | 125 | Pyrococcus Abyssi (Strain Ge5 / Orsay) , Pyrococcus Abyssi Ge5 , Synthetic Construct | MATFKLVISDPKTGIAKQIEITGPEAEKLIGKRIGDQIPVKELGINLNELFGKEFPEDVKMEIRGGTDKDGFPMRPDIHGPRRVRILLSKGPGFRPKEKGERRKKTVRGNTISPEIVQVNVKLVY |
| 30S ribosomal protein S8 | I | 130 | Pyrococcus Abyssi (Strain Ge5 / Orsay) , Pyrococcus Abyssi Ge5 , Synthetic Construct | MTLLDPLANALSHITNSERVGKREVYIKPASKLIGEVLRVMQKYGYIGEFEFIDDGRAGVYRVQLLGKINKAGAIKPRFPVKARDYERWEKRFLPAFEFGILIVSTSQGVMSHKEAREKGIGGRLIAYVY |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2019-09-20 Deposition Author(s): Coureux, P.-D. , Mechulam, Y. , Schmitt, E.