5U4I
Structural basis of co-translational quality control by arfa and rf2 bound to ribosome
PDB DOI: 10.2210/pdb5u4i/pdb
Classification: RIBOSOME
Organism(s): Escherichia Coli , Escherichia Coli (Strain K12) , Synthetic Construct
Deposited: 2016-12-04
Deposition Author(s): Chen, Y. , Jin, H. , Phillips, J.C. , Remis, J. , Shekhar, M. , Tajkhorshid, E. , Zeng, F.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY
Resolution: 3.5 Å
Structural basis of co-translational quality control by arfa and rf2 bound to ribosome
Chen, Y. , Jin, H. , Phillips, J.C. , Remis, J. , Shekhar, M. , Tajkhorshid, E. , Zeng, F.
Primary Citation of Related Structures: 5U4I
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 16S rRNA | a | 1533 | NA | AAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUUCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUUGACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCACGGUAAUACGGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCCUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGAAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUAGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCA |
| P-site or E-site fMet-tRNA(fMet) | x | 77 | NA | CGCGGGGUGGAGCAGCCUGGUAGCUCGUCGGGCUCAUAACCCGAAGGUCGUCGGUUCAAAUCCGGCCCCCGCAACCA |
| P-site or E-site fMet-tRNA(fMet) | y | 77 | NA | CGCGGGGUGGAGCAGCCUGGUAGCUCGUCGGGCUCAUAACCCGAAGGUCGUCGGUUCAAAUCCGGCCCCCGCAACCA |
| mRNA | z | 18 | NA | GGCAAGGAGGUAAAAAUG |
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 30S ribosomal protein S11 | K | 117 | Escherichia Coli , Escherichia Coli (Strain K12) , Synthetic Construct | RKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTPFAAQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHNGCRPPKKRRV |
| 30S ribosomal protein S12 | L | 123 | Escherichia Coli , Escherichia Coli (Strain K12) , Synthetic Construct | ATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNGFEVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGALDCSGVKDRKQARSKYGVKRPKA |
| 30S ribosomal protein S13 | M | 118 | Escherichia Coli , Escherichia Coli (Strain K12) , Synthetic Construct | MARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVAKFVVEGDLRREISMSIKRLMDLGCYRGLRHRRGLPVRGQRTKTNARTRKGPRKPIKK |
| 30S ribosomal protein S14 | N | 100 | Escherichia Coli , Escherichia Coli (Strain K12) , Synthetic Construct | AKQSMKAREVKRVALADKYFAKRAELKAIISDVNASDEDRWNAVLKLQTLPRDSSPSRQRNRCRQTGRPHGFLRKFGLSRIKVREAAMRGEIPGLKKASW |
| 30S ribosomal protein S15 | O | 88 | Escherichia Coli , Escherichia Coli (Strain K12) , Synthetic Construct | SLSTEATAKIVSEFGRDANDTGSTEVQVALLTAQINHLQGHFAEHKKDHHSRRGLLRMVSQRRKLLDYLKRKDVARYTQLIERLGLRR |
| 30S ribosomal protein S16 | P | 82 | Escherichia Coli , Escherichia Coli (Strain K12) , Synthetic Construct | MVTIRLARHGAKKRPFYQVVVADSRNARNGRFIERVGFFNPIASEKEEGTRLDLDRIAHWVGQGATISDRVAALIKEVNKAA |
| 30S ribosomal protein S17 | Q | 84 | Escherichia Coli , Escherichia Coli (Strain K12) , Synthetic Construct | MTDKIRTLQGRVVSDKMEKSIVVAIERFVKHPIYGKFIKRTTKLHVHDENNECGIGDVVEIRECRPLSKTKSWTLVRVVEKAVL |
| 30S ribosomal protein S18 | R | 75 | Escherichia Coli , Escherichia Coli (Strain K12) , Synthetic Construct | MARYFRRRKFCRFTEEGVQEIDYKDIATLKNYITESGKIVPSRITGTRAKYQRQLARAIKRARYLSLLPYTDRHQ |
| 30S ribosomal protein S19 | S | 82 | Escherichia Coli , Escherichia Coli (Strain K12) , Synthetic Construct | PRSLKKGPFIDLHLLKKVEKAVESGDKKPLRTWSRRSTIFPNMIGLTIAVHNGRQHVPVFVTDEMVGHKLGEFAPTRTYRGH |
| 30S ribosomal protein S20 | T | 86 | Escherichia Coli , Escherichia Coli (Strain K12) , Synthetic Construct | ANIKSAKKRAIQSEKARKHNASRRSMMRTFIKKVYAAIEAGDKAAAQKAFNEMQPIVDRQAAKGLIHKNKAARHKANLTAQINKLA |
| 30S ribosomal protein S2 | B | 241 | Escherichia Coli , Escherichia Coli (Strain K12) , Synthetic Construct | MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKIASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQSQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLGIPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEAE |
| 30S ribosomal protein S21 | U | 71 | Escherichia Coli , Escherichia Coli (Strain K12) , Synthetic Construct | MPVIKVRENEPFDVALRRFKRSCEKAGVLAEVRRREFYEKPTTERKRAKASAVKRHAKKLARENARRTRLY |
| Peptide chain release factor 2 | V | 383 | Escherichia Coli , Escherichia Coli (Strain K12) , Synthetic Construct | HHHHHHSAALEVLFQGPGMFEINPVNNRIQDLTERSDVLRGYLDYDAKKERLEEVNAELEQPDVWNEPERAQALGKERSSLEAVVDTLDQMKQGLEDVSGLLELAVEADDEETFNEAVAELDALEEKLAQLEFRRMFSGEYDSADCYLDIQAGSGGTEAQDWASMLERMYLRWAESRGFKTEIIEESEGEVAGIKSVTIKISGDYAYGWLRTETGVHRLVRKSPFDSGGRRHTSFSSAFVYPEVDDDIDIEINPADLRIDVYRTSGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKNKDQAMKQMKAKLYELEMQKKNAEKQAMEDNKSDIGWGSQIRSYVLDDSRIKDLRTGVETRNTQAVLDGSLDQFIEASLKAGL |
| Alternative ribosome-rescue factor A | W | 57 | Escherichia Coli , Escherichia Coli (Strain K12) , Synthetic Construct | GSMSRYQHTKGQIKDNAIEALLHDPLFRQRVEKNKKGKGSYMRKGKHGNRGNWEASG |
| 50S ribosomal protein L30 | 0 | 59 | Escherichia Coli , Escherichia Coli (Strain K12) , Synthetic Construct | MAKTIKITQTRSAIGRLPKHKATLLGLGLRRIGHTVEREDTPAIRGMINAVSFMVKVEE |
| 50S ribosomal protein L32 | 1 | 57 | Escherichia Coli , Escherichia Coli (Strain K12) , Synthetic Construct | MAVQQNKPTRSKRGMRRSHDALTAVTSLSVDKTSGEKHLRHHITADGYYRGRKVIAK |
| 50S ribosomal protein L33 | 2 | 55 | Escherichia Coli , Escherichia Coli (Strain K12) , Synthetic Construct | MAKGIREKIKLVSSAGTGHFYTTTKNKRTKPEKLELKKFDPVVRQHVIYKEAKIK |
| 50S ribosomal protein L34 | 3 | 46 | Escherichia Coli , Escherichia Coli (Strain K12) , Synthetic Construct | MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTVSK |
| 30S ribosomal protein S3 | C | 233 | Escherichia Coli , Escherichia Coli (Strain K12) , Synthetic Construct | MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERPAKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSITSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRADIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK |
| 50S ribosomal protein L35 | 4 | 65 | Escherichia Coli , Escherichia Coli (Strain K12) , Synthetic Construct | MPKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIACLPYA |
| 50S ribosomal protein L36 | 5 | 38 | Escherichia Coli , Escherichia Coli (Strain K12) , Synthetic Construct | MKVRASVKKLCRNCKIVKRDGVIRVICSAEPKHKQRQG |
| 50S ribosomal protein L3 | D | 209 | Escherichia Coli , Escherichia Coli (Strain K12) , Synthetic Construct | MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRVTKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSDLIVKPAVKA |
| 50S ribosomal protein L4 | E | 201 | Escherichia Coli , Escherichia Coli (Strain K12) , Synthetic Construct | MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPWRQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIVVEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSLIAFDKVVMTADAVKQVEEMLA |
| 50S ribosomal protein L5 | F | 179 | Escherichia Coli , Escherichia Coli (Strain K12) , Synthetic Construct | MAKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAISGQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAKSFDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTAKSDEEGRALLAAFDFPFRK |
| 50S ribosomal protein L6 | G | 177 | Escherichia Coli , Escherichia Coli (Strain K12) , Synthetic Construct | MSRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYADGWAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAGITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYADEVVRTKEAKKK |
| 50S ribosomal protein L9 | H | 149 | Escherichia Coli , Escherichia Coli (Strain K12) , Synthetic Construct | MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEARRAELEAKLAEVLAAANARAEKINALETVTIASKAGDEGKLFGSIGTRDIADAVTAAGVEVAKSEVRLPNGVLRTTGEHEVSFQVHSEVFAKVIVNVVAE |
| 30S ribosomal protein S9 | I | 130 | Escherichia Coli , Escherichia Coli (Strain K12) , Synthetic Construct | MAENQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEKLDLYITVKGGGISGQAGAIRHGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRKARRRPQFSKR |
| 50S ribosomal protein L11 | J | 142 | Escherichia Coli , Escherichia Coli (Strain K12) , Synthetic Construct | MAKKVQAYVKLQVAAGMANPSPPVGPALGQQGVNIMEFCKAFNAKTDSIEKGLPIPVVITVYADRSFTFVTKTPPAAVLLKKAAGIKSGSGKPNKDKVGKISRAQLQEIAQTKAADMTGADIEAMTRSIEGTARSMGLVVED |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2016-12-04
Deposition Author(s): Chen, Y. , Jin, H. , Phillips, J.C. , Remis, J. , Shekhar, M. , Tajkhorshid, E. , Zeng, F.