E. coli 50S with phazolicin (PHZ) bound in exit tunnel

2026-07-01 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY POLYMER_SEQUENCE entity_poly pdbx_audit_support _entity_poly.pdbx_seq_one_letter_code _pdbx_audit_support.funding_organization DATABASE_REFERENCES citation citation_author _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _citation_author.identifier_ORCID STRUCTURE_SUMMARY pdbx_molecule_features REFINEMENT_DESCRIPTION atom_site chem_comp_atom chem_comp_bond database_2 em_3d_fitting_list pdbx_initial_refinement_model pdbx_validate_rmsd_angle pdbx_validate_torsion struct_conn _atom_site.auth_atom_id _atom_site.label_atom_id _database_2.pdbx_DOI _database_2.pdbx_database_accession _em_3d_fitting_list.accession_code _em_3d_fitting_list.initial_refinement_model_id _em_3d_fitting_list.source_name _em_3d_fitting_list.type _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr2_label_atom_id STRUCTURE_SUMMARY atom_site chem_comp_atom chem_comp_bond em_admin pdbx_entry_details pdbx_modification_feature _atom_site.auth_atom_id _atom_site.label_atom_id _chem_comp_atom.atom_id _chem_comp_atom.pdbx_aromatic_flag _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.value_order _em_admin.last_update _pdbx_entry_details.has_protein_modification EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update RCSB RCSB 2019-08-23 2019-09-18 2019-09-18 2026-07-01 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM R01-114454 United States National Science Foundation (NSF, United States) 1106400 United States E. coli 50S with phazolicin (PHZ) bound in exit tunnel Watson ZL Cate JHD ribosome, phazolicin, antimicrobial protein, RIBOSOME-INHIBITOR complex Travin DY Watson ZL Metelev M Ward FR Osterman IA Khven IM Khabibullina NF Serebryakova M Mergaert P Polikanov YS Cate JHD Severinov K Structure of ribosome-bound azole-modified peptide phazolicin rationalizes its species-specific mode of bacterial translation inhibition. Nat Commun UK 10 4563 4563 2019 31594941 doi:10.1038/s41467-019-12589-5 2041-1723 6u48 FULLOVERLAP EMDB EMD-20638 associated EM volume

E. coli ribosome with phazolicin in exit tunnel E. coli ribosome with phazolicin in exit tunnel 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32

Ribosomal small subunit is not modeled due to poor density in reconstruction

E. coli 50S 1 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 Escherichia coli Phazolicin 1 32 Rhizobium sp. Pop5 23S rRNA Escherichia coli 0.941092125 1 GGUUAAGCGACUAAGCGUACACGGUGGAUGCCCUGGCAGUCAGAGGCGAUGAAGGACGUGCUAAUCUGCGAUAAGCGUCG GUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUUCCGAAUGGGGAAACCCAGUGUGUUUCGACACACUAUCAUUAACUGA AUCCAUAGGUUAAUGAGGCGAACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCC AGUAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCUGAAUCAGUGUGUGUGUUAGUGGAAGCGUCUGGAAAGGCGCGCGA UACAGGGUGACAGCCCCGUACACAAAAAUGCACAUGCUGUGAGCUCGAUGAGUAGGGCGGGACACGUGGUAUCCUGUCUG AAUAUGGGGGGACCAUCCUCCAAGGCUAAAUACUCCUGACUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGCGAAAA GAACCCCGGCGAGGGGAGUGAAAAAGAACCUGAAACCGUGUACGUACAAGCAGUGGGAGCACGCUUAGGCGUGUGACUGC GUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAGCAAGGUUAACCGAAUAGGGGAGCCGAAGGGAAACCGAGUC UUAACUGGGCGUUAAGUUGCAGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACU AACUGGAGGACCGAACCGACUAAU(1MG)(PSU)(5MU)GAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUGAAAGGCCA AUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUCGUGAAUUCAUCUCCGGGGGUAGAGCACU GUUUCGGCAAGGGGGUC(N)(N)(N)(N)(N)(N)ACUUACCAACCCGAUGCAAACUGCGAAUACCGGAGAAUGUUAUCA CGGGAGACACACGGCGGG(PSU)GCUAACGUCCGUCGUGAAGAGGGAAACAACCCAGACCGCCAGCUAAGGUCCCAAAGU CAUGGUUAAGUGGGAAACGAUGUGGGAAGGCCCAGACAGCCAGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAAAGC GUAAUAGCUCACUGGUCGAGUCGGCCUGCGCGGAAGAUGUAACGGGGCUAAACCAUGCACCGAAGCUGCGGCAGCGACGC UUAUGCGUUGUUGGGUAGGGGAGCGUUCUGUAAGCCUGCGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAAGUGCG AAUGCUGACAUAAGUAACGAUAAAGCGGGUGAAAAGCCCGCUCGCCGGAAGACCAAGGGUUCCUGUCCAACGUUAAUCGG GGCAGGGUGAGUCGACCCCUAAGGCGAGGCCGAAAGGCGUAGUCGAUGGGAAACAGGUUAAUAUUCCUGUACUUGGUGUU ACUGCGAAGGGGGGACGGAGAAGGCUAUGUUGGCCGGGCGACGGUUGUCCCGGUUUAAGCGUGUAGGCUGGUUUUCCAGG CAAAUCCGGAAAAUCAAGGCUGAGGCGUGAUGACGAGGCACUACGGUGCUGAAGCAACAAAUGCCCUGCUUCCAGGAAAA GCCUCUAAGCAUCAGGUAACAUCAAAUCGUACCCCAAACCGACAC(6MZ)GGUGGUCAGGUAGAGAAUACCAAGGCGCUU GAGAGAACUCGGGUGAAGGAACUAGGCAAAAUGGUGCCGUAACUUCGGGAGAAGGCACGCUGAUAUGUAGGUGAGGUCCC UCGCGGAUGGAGCUGAAAUCAGUCGAAGAUACCAGCUGGCUGCAACUGUUUAUUAAAAACACAGCACUGUGCAAACACGA AAGUGGACGUAUACGGUGUGACGCCU(2MG)CCCGGUGCCGGAAGGUUAAUUGAUGGGGUUAGCGCAAGCGAAGCUCUUG AUCGAAGCCCCGGUAAACGGCGGCCG(PSU)AAC(3TD)A(PSU)AACGGUCCUAAGGUAGCGAAA(5MU)UCCUUGUCG GGUAAGUUCCGAC(5MC)UGCACGAAUGGCGUAAUGAUGGCCAGGCUGUCUCCACCCGAGACUCAGUGAAAUUGAACUCG CUGUG(6MZ)AGAUGCAGUGUACCCGCGGCAAGACGGAAAGACCCCGU(G7M)AACCUUUACUAUAGCUUGACACUGAAC AUUGAGCCUUGAUGUGUAGGAUAGGUGGGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGGAGCCGACCUUGAAAUACCA CCCUUUAAUGUUUGAUGUUCUAACGUUGACCCGUAAUCCGGGUUGCGGACAGUGUCUGGUGGGUAGUUUGACUG(OMG)G GCGGUCUCCUCCUAAAGAGUAACGGAGGAGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGC AUAAGCCAGCUUGACUGCGAGCGUGACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGGUUCUGAAUGGAA GGGCCAUCGCUCAACGGAUAAAAGGUACUCCG(2MG)GGA(H2U)AACAGGC(PSU)GAUACCGCCCAAGAGUUCAUAUC GACGGCGGUGUUUGGCA(OMC)CUCG(2MA)(PSU)GUCGGCUCAUCACAUCCUGGGGCUGAAGUAGGUCCCAAGGGUAU GGC(OMU)GUUCGCCAUUUAAAGUGGUACGCGAGC(PSU)GGGUUUAGAACGUCGUGAGACAGU(PSU)CGGUCCCUAUC UGCCGUGGGCGCUGGAGAACUGAGGGGGGCUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUU GUCAUGCCAAUGGCACUGCCCGGUAGCUAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCUAAGCACGAAACUUGCCCCGA GAUGAGUUCUCCCUGACCCUUUAAGGGUCCUGAAGGAACGUUGAAGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCA GCGAUGCGUUGAGCUAACCGGUACUAAUGAACCGUGAGGCUUAACCUU 5S rRNA Escherichia coli 0.038177762000000004 1 GCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAACGCCGUAGCGCCGAUGGUAGUG UGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCA CP023870.1 50S ribosomal protein uL2 Escherichia coli 0.029663244 1 LEVO AVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQAYRIVDFKRNKDGIPAVVERL EYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGVDAAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTY VQIVARDGAYVTLRLRSGEMRKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNFG KHPVTPWGVQTKGKKTRSNKRTDKFIVRRRS A0A1X3I1Y9 50S ribosomal protein uL3 Escherichia coli 0.022291562 1 LEVO MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRVTKPEAGHFAKAGVEAGRGLW EFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQN(MEQ)TPGKVF KGKKMAGQMGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSDLIVKPAVKA A0A1X3JBR5 50S ribosomal protein uL4 Escherichia coli 0.022121566 1 LEVO MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPWRQKGTGRARSGSIKSPIWRS GGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIVVEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLA ARNLHKVDVRDATGIDPVSLIAFDKVVMTADAVKQVEEMLA D7Z9F6 50S ribosomal protein uL5 Escherichia coli 0.020073234 1 LEVO AKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAISGQKPLITKARKSVAGFKIRQ GYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAKSFDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTAK SDEEGRALLAAFDFPFR V8K465 50S ribosomal protein uL6 Escherichia coli 0.018801598 1 LEVO SRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYADGWAQAGTARALLNSMVIGVTE GFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAGITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKG VRYADEVVRTKEAKKK A0A080FKA9 50S ribosomal protein bL9 Escherichia coli 0.01578902 1 LEVO MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEARRAELEAKLAEVLAAANARAEKINALETVTI ASKAGDEGKLFGSIGTRDIADAVTAAGVEVAKSEVRLPNGVLRTTGEHEVSFQVHSEVFAKVIVNVVAE D7ZI15 50S ribosomal protein uL11 Escherichia coli 0.014020303 1 LEVO YVKLQVAAGMANPSPPVGPALGQQGVNIMEFCKAFNAKTDSIEKGLPIPVVITVYADRSFTFVTKTPPAAVLLKKAAGIK SGSGKPNKDKVGKISRAQLQEIAQTKAADMTGADIEAMTRSIEGTARSMGLVVE H4KQ36 50S ribosomal protein uL13 Escherichia coli 0.016050606 1 LEVO MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNADKVAVTGNKRTDKVYYHHTGH IGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFRKLKVYAGNEHNHAAQQPQVLDI D7ZET0 50S ribosomal protein uL14 Escherichia coli 0.01345191 1 LEVO MIQEQTMLNVADNSGARRVMCIKVLGGSHRRYAGVGDIIKITIKEAIPRGKVKKGDVLKAVVVRTKKGVRRPDGSVIRFD GNACVLLNNNSEQPIGTRIFGPVTRELRSEKFMKIISLAPEV A0A140N3H4 50S ribosomal protein uL15 Escherichia coli 0.015008470999999999 1 LEVO MRLNTLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGFEGGQMPLYRRLPKFGFTSRKAAITAEIRLS DLAKVEGGVVDLNTLKAANIIGIQIEFAKVILAGEVTTPVTVRGLRVTKGARAAIEAAGGKIEE A0A037Y8L6 50S ribosomal protein uL16 Escherichia coli 0.015327261 1 LEVO MLQPKRTKFRKMHKGRNRGLAQGTDVSFGSFGLKAVGRGRLTARQIEAARRAMTRAVKRQGKIWIRVFPDKPITEKPLAV (4D4)MGKGKGNVEYWVALIQPGKVLYEMDGVPEELAREAFKLAAAKLPIKTTFVTKTVM J7RVN4 50S ribosomal protein bL17 Escherichia coli 0.013721938 1 LEVO MRHRKSGRQLNRNSSHRQAMFRNMAGSLVRHEIIKTTLPKAKELRRVVEPLITLAKTDSVANRRLAFARTRDNEIVAKLF NELGPRFASRAGGYTRILKCGFRAGDNAPMAYIELVDRSE A0A0A8UJP9 50S ribosomal protein uL18 Escherichia coli 0.012663470999999999 1 LEVO DKKSARIRRATRARRKLQELGATRLVVHRTPRHIYAQVIAPNGSEVLVAASTVEKAIAEQLKYTGNKDAAAAVGKAVAER ALEKGIKDVSFDRSGFQYHGRVQALADAAREAGLQF I2X628 50S ribosomal protein bL19 Escherichia coli 0.013028082 1 LEVO SNIIKQLEQEQMKQDVPSFRPGDTVEVKVWVVEGSKKRLQAFEGVVIAIRNRGLHSAFTVRKISNGEGVERVFQTHSPVV DSISVKRRGAVRKAKLYYLRERTGKAARIKERLN L2UTN8 50S ribosomal protein bL20 Escherichia coli 0.013396828 1 LEVO ARVKRGVIARARHKKILKQAKGYYGARSRVYRVAFQAVIKAGQYAYRDRRQRKRQFRQLWIARINAAARQNGISYSKFIN GLKKASVEIDRKILADIAVFDKVAFTALVEKAKAALA I2RGN4 50S ribosomal protein bL21 Escherichia coli 0.011586374 1 LEVO MYAVFQSGGKQHRVSEGQTVRLEKLDIATGETVEFAEVLMIANGEEVKIGVPFVDGGVIKAEVVAHGRGEKVKIVKFRRR KHYRKQQGHRQWFTDVKITGISA D7ZEN7 50S ribosomal protein uL22 Escherichia coli 0.012253359 1 LEVO METIAKHRHARSSAQKVRLVADLIRGKKVSQALDILTYTNKKAAVLVKKVLESAIANAEHNDGADIDDLKVTKIFVDEGP SMKRIMPRAKGRADRILKRTSHITVVVSDR D7Z9G0 50S ribosomal protein uL23 Escherichia coli 0.010546472 1 LEVO MIREERLLKVLRAPHVSEKASTAMEKSNTIVLKVAKDATKAEIKAAVQKLFEVEVEVVNTLVVKGKVKRHGQRIGRRSDW KKAYVTLKEGQNL H4IXX7 50S ribosomal protein uL24 Escherichia coli 0.011078873999999999 1 LEVO AAKIRRDDEVIVLTGKDKGKRGKVKNVLSSGKVIVEGINLVKKHQKPVPALNQPGGIVEKEAAIQVSNVAIFNAATGKAD RVGFRFEDGKKVRFFKSNSETI A0A0G3K7Z5 50S ribosomal protein bL25 Escherichia coli 0.010713465 1 LEVO MFTINAEVRKEQGKGASRRLRAANKFPAIIYGGKEAPLAIELDHDKVMNMQAKAEFYSEVLTIVVDGKEIKVKAQDVQRH PYKPKLQHIDFVRA D7XH79 50S ribosomal protein bL27 Escherichia coli 0.008174394 1 LEVO RNGRDSEAKRLGVKRFGGESVLAGSIIVRQRGTKFHAGANVGCGRDHTLFAKADGKVKFEVKGPKNRKFISIEAE A0A1X3JCC7 50S ribosomal protein bL28 Escherichia coli 0.008896353999999999 1 LEVO SRVCQVTGKRPVTGNNRSHALNATKRRFLPNLHSHRFWVESEKRFVTLRVSAKGMRVIDKKGIDTVLAELRARGEKY V8F9Y0 50S ribosomal protein uL29 Escherichia coli 0.007155267 1 LEVO KAKELREKSVEELNTELLNLLREQFNLRMQAASGQLQQSHLLKQVRRDVARVKTLLNEKAGA D8E8E5 50S ribosomal protein uL30 Escherichia coli 0.006423625 1 LEVO AKTIKITQTRSAIGRLPKHKATLLGLGLRRIGHTVEREDTPAIRGMINAVSFMVKVEE A0A073UEE9 50S ribosomal protein bL32 Escherichia coli 0.006332249 1 LEVO AVQQNKPTRSKRGMRRSHDALTAVTSLSVDKTSGEKHLRHHITADGYYRGRKVIAK V0ZMP5 50S ribosomal protein bL33 Escherichia coli 0.005814842 1 LEVO GIREKIKLVSSAGTGHFYTTTKNKRTKPEKLELKKFDPVVRQHVIYKEAK L4V2B0 50S ribosomal protein bL34 Escherichia coli 0.005397463 1 LEVO MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTVSK B7MGC4 50S ribosomal protein bL35 Escherichia coli 0.007181835 1 LEVO PKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIACLPYA I2RJ64 50S ribosomal protein bL36 Escherichia coli 0.00437739 1 LEVO MKVRASVKKLCRNCKIVKRDGVIRVICSAEPKHKQRQG A0A0E2L017 phazolicin Rhizobium sp. Pop5 0.002054102 1 LEVO T(BB9)AR(BB9)DS(A0G)SR(BB9)GA(A0G)GK(A0G)SG(A0G)AS singleParticle particle 7.5

unspecified

ETHANE FEI TITAN KRIOS OTHER BRIGHT FIELD FIELD EMISSION GUN 300 2.7 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K2 SUMMIT (4k x 4k) 30.0 1 CTFFIND 4 PHASE FLIPPING AND AMPLITUDE CORRECTION 4YBB 2.87 FSC 0.143 CUT-OFF RELION 65393 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_20638.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 -54 -84 -90 320 320 320 356.352 356.352 356.352 90.0 90.0 90.0 X Y Z -0.14081855 0.21396987 -0.00000004051004 0.0077487044 1.1136 1.1136 1.1136 0.027 AUTHOR ::::EMDATABANK.org::::EMD-20638:::: Charge density map used for real space refine, obtained as described by Wang, J. (2017) 4YBB PDB experimental model emd_20638_msk_1.map emd_20638_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 -54 -84 -90 320 320 320 356.352 356.352 356.352 90.0 90.0 90.0 X Y Z -0.13638425 0.24741457 -0.000040575917 0.008663437 1.1136 1.1136 1.1136 AUTHOR ::::EMDATABANK.org::::EMD-20638:::: RELION post-processed map, used for preview image emd_20638_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 -54 -84 -90 320 320 320 356.352 356.352 356.352 90.0 90.0 90.0 X Y Z -0.029948317 0.09023676 -0.0000987193 0.0037048708 1.1136 1.1136 1.1136 AUTHOR ::::EMDATABANK.org::::EMD-20638:::: RELION 3D auto-refine map emd_20638_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 -54 -84 -90 320 320 320 356.352 356.352 356.352 90.0 90.0 90.0 X Y Z -0.047126144 0.11810611 -0.00003981128 0.0065078023 1.1136 1.1136 1.1136 AUTHOR ::::EMDATABANK.org::::EMD-20638:::: half map #2 emd_20638_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 -54 -84 -90 320 320 320 356.352 356.352 356.352 90.0 90.0 90.0 X Y Z -0.04796026 0.11071637 -0.00004134055 0.0065199165 1.1136 1.1136 1.1136 AUTHOR ::::EMDATABANK.org::::EMD-20638:::: half map #1