5L3P
Cryo-em structure of stringent response factor rela bound to ermcl-stalled ribosome complex
PDB DOI: 10.2210/pdb5l3p/pdb
Classification: RIBOSOME Organism(s): Escherichia Coli , Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Escherichia Coli K12 , Escherichia Coli O157:H7 , Synthetic Construct
Deposited: 2016-05-24 Deposition Author(s): Arenz, S. , Wilson, D.N.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 3.7 Å
Cryo-em structure of stringent response factor rela bound to ermcl-stalled ribosome complex
Primary Citation of Related Structures: 5L3P
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 16S ribosomal RNA | a | 1539 | NA | AAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUUCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUUGACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCCUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGAAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUAGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCU |
| mRNA | v | 6 | NA | AUAAUG |
| P-site tRNA | x | 77 | NA | CGCGGGGUGGAGCAGCCUGGUAGCUCGUCGGGCUCAUAACCCGAAGAUCGUCGGUUCAAAUCCGGCCCCCGCAACCA |
| deacylated A/R-tRNA | y | 73 | NA | GCUGAUAUAGCUCAGUUGGUAGAGCGCACCCUUGGUGAGGGUGAGGUCGGCAGUUCGAAUCUGCCUAUCAGCA |
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 30S ribosomal protein S15 | O | 89 | Escherichia Coli , Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Escherichia Coli K12 , Escherichia Coli O157:H7 , Synthetic Construct | MSLSTEATAKIVSEFGRDANDTGSTEVQVALLTAQINHLQGHFAEHKKDHHSRRGLLRMVSQRRKLLDYLKRKDVARYTQLIERLGLRR |
| 30S ribosomal protein S16 | P | 82 | Escherichia Coli , Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Escherichia Coli K12 , Escherichia Coli O157:H7 , Synthetic Construct | MVTIRLARHGAKKRPFYQVVVADSRNARNGRFIERVGFFNPIASEKEEGTRLDLDRIAHWVGQGATISDRVAALIKEVNKAA |
| 30S ribosomal protein S17 | Q | 84 | Escherichia Coli , Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Escherichia Coli K12 , Escherichia Coli O157:H7 , Synthetic Construct | MTDKIRTLQGRVVSDKMEKSIVVAIERFVKHPIYGKFIKRTTKLHVHDENNECGIGDVVEIRECRPLSKTKSWTLVRVVEKAVL |
| 30S ribosomal protein S18 | R | 75 | Escherichia Coli , Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Escherichia Coli K12 , Escherichia Coli O157:H7 , Synthetic Construct | MARYFRRRKFCRFTAEGVQEIDYKDIATLKNYITESGKIVPSRITGTRAKYQRQLARAIKRARYLSLLPYTDRHQ |
| 30S ribosomal protein S19 | S | 92 | Escherichia Coli , Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Escherichia Coli K12 , Escherichia Coli O157:H7 , Synthetic Construct | MPRSLKKGPFIDLHLLKKVEKAVESGDKKPLRTWSRRSTIFPNMIGLTIAVHNGRQHVPVFVTDEMVGHKLGEFAPTRTYRGHAADKKAKKK |
| 30S ribosomal protein S20 | T | 87 | Escherichia Coli , Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Escherichia Coli K12 , Escherichia Coli O157:H7 , Synthetic Construct | MANIKSAKKRAIQSEKARKHNASRRSMMRTFIKKVYAAIEAGDKAAAQKAFNEMQPIVDRQAAKGLIHKNKAARHKANLTAQINKLA |
| 30S ribosomal protein S21 | U | 71 | Escherichia Coli , Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Escherichia Coli K12 , Escherichia Coli O157:H7 , Synthetic Construct | MPVIKVRENEPFDVALRRFKRSCEKAGVLAEVRRREFYEKPTTERKRAKASAVKRHAKKLARENARRTRLY |
| 50S ribosomal protein L22 | W | 110 | Escherichia Coli , Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Escherichia Coli K12 , Escherichia Coli O157:H7 , Synthetic Construct | METIAKHRHARSSAQKVRLVADLIRGKKVSQALDILTYTNKKAAVLVKKVLESAIANAEHNDGADIDDLKVTKIFVDEGPSMKRIMPRAKGRADRILKRTSHITVVVSDR |
| 30S ribosomal protein S2 | B | 240 | Escherichia Coli , Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Escherichia Coli K12 , Escherichia Coli O157:H7 , Synthetic Construct | MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKIASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQSQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLGIPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEA |
| GTP pyrophosphokinase,GTP pyrophosphokinase,GTP pyrophosphokinase | Z | 819 | Escherichia Coli , Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Escherichia Coli K12 , Escherichia Coli O157:H7 , Synthetic Construct | MVAVRSAHINKAGEFDPEKWIASLGITSQKSCECLAETWAYCLQQTQGHPDASLLLWRGVEMVEILSTLSMDIDTLRAALLFPLADANVVSEDVLRESVGKSVVNLIHGVRDMAAIRQLKATHTDSVSSEQVDNVRRMLLAMVDDFRCVVIKLAERIAHLREVKDAPEDERVLAAKECTNIYAPLANRLGIGQLKWELEDYCFRYLHPTEYKRIAKLLHERRLDREHYIEEFVGHLRAEMKAEGVKAEVYGRPKHIYSIWRKMQKKNLAFDELFDVRAVRIVAERLQDCYAALGIVHTHYRHLPDEFDDYVANPKPNGYQSIHTVVLGPGGKTVEIQIRTKQMHEDAELGVAAHWKYKEGAAAGGARSGHEDRIAWLRKLIAWQEEMADSGEMLDEVRSQVFDDRVYVFTPKGDVVDLPAGSTPLDFAYHIHSDVGHRCIGAKIGGRIVPFTYQLQMGDQIEIITQKQPNPSRDWLNPNLGYVTTSRGRSKIHAWFRKQDRDKNILAGRQILDDELEHLGISLKEAEKHLLPRYNFNDVDELLAAIGGGDIRLNQMVNFLQSQFNKPSAEEQDAAALKQLQQKSYTPQNRSKDNGRVVVEGVGNLMHHIARCCQPIPGDEIVGFITQGRGISVHRADCEQLAELRSHAPERIVDAVWGESYSXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXAGYSLVVRVVANDRSGLLRDITTILANEKVNVLGVASRSDTKQQLATIDMTIEIYNLQVLGRVLGKLNQVPDVIDARRLHGS |
| 50S ribosomal protein L27 | 0 | 85 | Escherichia Coli , Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Escherichia Coli K12 , Escherichia Coli O157:H7 , Synthetic Construct | MAHKKAGGSTRNGRDSEAKRLGVKRFGGESVLAGSIIVRQRGTKFHAGANVGCGRDHTLFAKADGKVKFEVKGPKNRKFISIEAE |
| 50S ribosomal protein L28 | 1 | 78 | Escherichia Coli , Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Escherichia Coli K12 , Escherichia Coli O157:H7 , Synthetic Construct | MSRVCQVTGKRPVTGNNRSHALNATKRRFLPNLHSHRFWVESEKRFVTLRVSAKGMRVIDKKGIDTVLAELRARGEKY |
| 50S ribosomal protein L29 | 2 | 63 | Escherichia Coli , Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Escherichia Coli K12 , Escherichia Coli O157:H7 , Synthetic Construct | MKAKELREKSVEELNTELLNLLREQFNLRMQAASGQLQQSHLLKQVRRDVARVKTLLNEKAGA |
| 50S ribosomal protein L30 | 3 | 59 | Escherichia Coli , Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Escherichia Coli K12 , Escherichia Coli O157:H7 , Synthetic Construct | MAKTIKITQTRSAIGRLPKHKATLLGLGLRRIGHTVEREDTPAIRGMINAVSFMVKVEE |
| 50S ribosomal protein L31 | 4 | 70 | Escherichia Coli , Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Escherichia Coli K12 , Escherichia Coli O157:H7 , Synthetic Construct | MKKDIHPKYEEITASCSCGNVMKIRSTVGHDLNLDVCSKCHPFFTGKQRDVATGGRVDRFNKRFNIPGSK |
| 50S ribosomal protein L32 | 5 | 57 | Escherichia Coli , Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Escherichia Coli K12 , Escherichia Coli O157:H7 , Synthetic Construct | MAVQQNKPTRSKRGMRRSHDALTAVTSLSVDKTSGEKHLRHHITADGYYRGRKVIAK |
| 50S ribosomal protein L33 | 6 | 55 | Escherichia Coli , Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Escherichia Coli K12 , Escherichia Coli O157:H7 , Synthetic Construct | MAKGIREKIKLVSSAGTGHFYTTTKNKRTKPEKLELKKFDPVVRQHVIYKEAKIK |
| 50S ribosomal protein L34 | 7 | 46 | Escherichia Coli , Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Escherichia Coli K12 , Escherichia Coli O157:H7 , Synthetic Construct | MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTVSK |
| 30S ribosomal protein S4 | D | 206 | Escherichia Coli , Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Escherichia Coli K12 , Escherichia Coli O157:H7 , Synthetic Construct | MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQKVRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEGTFKRKPERSDLSADINEHLIVELYSK |
| 50S ribosomal protein L35 | 8 | 65 | Escherichia Coli , Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Escherichia Coli K12 , Escherichia Coli O157:H7 , Synthetic Construct | MPKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIACLPYA |
| 50S ribosomal protein L36 | 9 | 38 | Escherichia Coli , Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Escherichia Coli K12 , Escherichia Coli O157:H7 , Synthetic Construct | MKVRASVKKLCRNCKIVKRDGVIRVICSAEPKHKQRQG |
| 30S ribosomal protein S3 | C | 233 | Escherichia Coli , Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Escherichia Coli K12 , Escherichia Coli O157:H7 , Synthetic Construct | MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERPAKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSITSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRADIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK |
| 50S ribosomal protein L3 | E | 209 | Escherichia Coli , Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Escherichia Coli K12 , Escherichia Coli O157:H7 , Synthetic Construct | MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRVTKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSDLIVKPAVKA |
| 50S ribosomal protein L4 | F | 201 | Escherichia Coli , Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Escherichia Coli K12 , Escherichia Coli O157:H7 , Synthetic Construct | MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPWRQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIVVEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSLIAFDKVVMTADAVKQVEEMLA |
| 50S ribosomal protein L5 | G | 179 | Escherichia Coli , Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Escherichia Coli K12 , Escherichia Coli O157:H7 , Synthetic Construct | MAKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAISGQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAKSFDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTAKSDEEGRALLAAFDFPFRK |
| 50S ribosomal protein L6 | H | 177 | Escherichia Coli , Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Escherichia Coli K12 , Escherichia Coli O157:H7 , Synthetic Construct | MSRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYADGWAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAGITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYADEVVRTKEAKKK |
| 50S ribosomal protein L9 | I | 149 | Escherichia Coli , Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Escherichia Coli K12 , Escherichia Coli O157:H7 , Synthetic Construct | MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEARRAELEAKLAEVLAAANARAEKINALETVTIASKAGDEGKLFGSIGTRDIADAVTAAGVEVAKSEVRLPNGVLRTTGEHEVSFQVHSEVFAKVIVNVVAE |
| 50S ribosomal protein L10 | J | 165 | Escherichia Coli , Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Escherichia Coli K12 , Escherichia Coli O157:H7 , Synthetic Construct | MALNLQDKQAIVAEVSEVAKGALSAVVADSRGVTVDKMTELRKAGREAGVYMRVVRNTLLRRAVEGTPFECLKDAFVGPTLIAYSMEHPGAAARLFKEFAKANAKFEVKAAAFEGELIPASQIDRLATLPTYEEAIARLMATMKEASAGKLVRTLAAVRDAKEAA |
| 50S ribosomal protein L11 | K | 142 | Escherichia Coli , Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Escherichia Coli K12 , Escherichia Coli O157:H7 , Synthetic Construct | MAKKVQAYVKLQVAAGMANPSPPVGPALGQQGVNIMEFCKAFNAKTDSIEKGLPIPVVITVYADRSFTFVTKTPPAAVLLKKAAGIKSGSGKPNKDKVGKISRAQLQEIAQTKAADMTGADIEAMTRSIEGTARSMGLVVED |
| 30S ribosomal protein S12 | L | 124 | Escherichia Coli , Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Escherichia Coli K12 , Escherichia Coli O157:H7 , Synthetic Construct | MATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNGFEVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGALDCSGVKDRKQARSKYGVKRPKA |
| 30S ribosomal protein S13 | M | 118 | Escherichia Coli , Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Escherichia Coli K12 , Escherichia Coli O157:H7 , Synthetic Construct | MARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVAKFVVEGDLRREISMSIKRLMDLGCYRGLRHRRGLPVRGQRTKTNARTRKGPRKPIKK |
| 50S ribosomal protein L13 | N | 142 | Escherichia Coli , Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Escherichia Coli K12 , Escherichia Coli O157:H7 , Synthetic Construct | MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNADKVAVTGNKRTDKVYYHHTGHIGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFRKLKVYAGNEHNHAAQQPQVLDI |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2016-05-24 Deposition Author(s): Arenz, S. , Wilson, D.N.