2025-05-28 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name STRUCTURE_SUMMARY chem_comp entity _chem_comp.formula _chem_comp.formula_weight _entity.formula_weight STRUCTURE_SUMMARY chem_comp chem_comp_atom chem_comp_bond database_2 em_admin pdbx_entry_details pdbx_modification_feature struct_conn _chem_comp.pdbx_synonyms _database_2.pdbx_DOI _database_2.pdbx_database_accession _em_admin.last_update _struct_conn.pdbx_dist_value _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_seq_id DATA_COLLECTION em_admin em_software _em_admin.last_update _em_software.name RCSB RCSB 2017-09-09 2017-12-06 2017-12-06 2025-05-28 Shalev-Benami M Zhang Y Leishmania donovani, ribosome, aminoglycoside, paromomycin, RIBOSOME-ANTIBIOTIC complex Shalev-Benami M Zhang Y Rozenberg H Nobe Y Taoka M Matzov D Zimmerman E Bashan A Isobe T Jaffe CL Yonath A Skiniotis G Nat Commun UK 8 1589 1589 2017 29150609 doi:10.1038/s41467-017-01664-4 2041-1723 EMD-7025 other EM volume

Cryo-EM structure of the large subunit of Leishmania ribosome bound to paromomycin

6az1 FULLOVERLAP Leishmania donovani 91S ribosome SSU Leishmania donovani 91S ribosome SSU 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 33 34 35 36 37 38 Leishmania donovani Ribosomal protein s1e Leishmania donovani 0.030092063999999998 1 LEVO MALGKNKRISKGGKRSKRGKAQETMARKEWYDVVAPANFEKRQFAKTICNKTQGTRIAADVLRGRVFEANLADLNQSAGE EEAYRKVRFTVQEVQGRNLLTQFHSMEVTTDKMASLLRKWCTTMETTVEVKTADGYTMRLFVVAFTKPQANQQSRNCYAK QRLVKWLRMRITKMIKRRLSKVQIKEAVSLLTRNVLSDALVRRCNPILPLRELRIRKVRVVRTPKFDAQALLSAHGTIPA SVEADQREVEEAVEAAPAAEKAAE E9BRS2 ribosomal protein S2 Leishmania donovani 0.027564682 1 LEVO MTAVESGSKVLRMKESDAQKLLAMRCHIGTRNQSSAMKKYIYGRTAEGSHIIDLHMMWEKLILAARVIAAVENPKDVCVC SSRLYGTRAIYKFSQHVGTSFHGGRFIPGTFTNQIQKKFVQPRVLVVTDPRTDHQAIREASLVNIPVIALCDTDAPLEYV DIAIPCNNRGIKSIGMMYWLLAREVLRLRGTIVRSVPWEEKVDLFFYRDPNEAAEEKAAAAAAAPAAEAEEGFGWVERND DNAWEA ribosomal protein S3 Leishmania donovani 0.024511761999999996 1 LEVO MGPLSKKRMIIRDGVFYAELFEFLKRELAEEGFSGVSYHVTTLRTEIVIKATKTREVLGVNGRRIRELTACIQQRFNYKE GKLQLYVERVEVRGLSAMAQVESLRFKLLSNLQVRRAAMGIIRYVMESGAKGCEVTVGGKIKGQRAKSMTFRDGYMIKSG TAHKSFVDSACRHCYMRAGCIGVKVKIMLPGDSTGRNGPSEPLPDVITVIEPKQITASE E9BQ25 ribosomal protein S4 Leishmania donovani 0.022184914 1 LEVO MRNYNNFNRVWKAPRRPFEKERLDREMKLCGQYGLRCKREIWRVNMTLSKMRRTARLLLTLPENHPRRLLEGSAIMRRCH EYGFLDEEKDKLDYVLSLTVPDILERRLQTIVFKAGLAKSVHHARVLIQQRHIAVAKQIVTIPSFIVRVSSERHIAFADA SPFGNGRPGRVKRVRAKAAKRHAGGGDDDE E9BTJ0 ribosomal protein S4e Leishmania donovani 0.030711087999999997 1 LEVO MAKKHLKRLYAPKDWMLSKLTGVFAPRPRPGPHKLRECLPLLVIIRNRLKYALNAREGEMILRQGLVHVDNHPRRDGKYP AGFMDVVEIPKTGDRFRLMYDVKGRFALVSLSEAEAQIKLMKVVNLYTATGRVPVAVTHDGHRIRYPDPHTSIGDTIVYN VKEKKCVDLIKNRQGKAVIVTGGANRGRIGEIVKVECHPGAFNIAHLKDASGAEFATRAANIFVIGKDLNHLQVTVPKQQ GLRMNVIQEREERLIAAEARKNAPARGARKARK E9BBI6 ribosomal protein S5 Leishmania donovani 0.028803186 1 LEVO MADTQPAQEAPAADVPRAERNFGRGRGGRGGRGRGRGGPGEEKEWVPCTKLGRLVKAQKVTSLEEIFLFSMPIKEHQIVD TLIAEGQLHDEMMKIYPVQKATSAGQRTRFKAFNVVGDCDGHIGIGARVGKEVSLAIRASMIAAKLNIVPVRRGYWGNKI GEPHTIPMKVTGKCGSVAVRLVPAPRGTGIVAAPVPKKILEFAGVEDVYTSSRGKTRTHGNLIMATFYALRKTYGFLTPD LWAETEPSRDPTDEHAELLAEMTTA E9BNF0 ribosomal protein S6e Leishmania donovani 0.028341164 1 LEVO MKLNIAYPRNGTVKQFEISDEVLRRVQLQDYRLGNEVDGAIFGSEFKGYIFRLRGGSDKDGFPMVPGVLASSRVSLLVKR GAIGFNTFRGYQGERRRKNVRGCVLASDIALVNVTISKVGDQPIEGVTDTTAPRRLGPKRASKIRKLFNLSRTEDVRKYV VRRRVVKSGKKDRLKAPKIQRLITPRVKARRAKKAKDAIAKVRASAAERREYLRLIASNRRALRQRDHSKKHTQKVHAQR AEVAAFQKK ribosomal protein S7 Leishmania donovani 0.021311596000000002 1 LEVO MSSKTPKLFNKWSFEGLETSELALRDHISTTAAYVPHTSGRWQKRRFHKARMPIVERLANGLMFKGRGNGRKLQAARLLK HTLEIIHLLTDENPLQVVVDAVSKGAPREDSTRVGSGGVVRRQAVDVSPMRRVNEAIYQMCKGAREAAFRNLKSMPECLA DEIVNASKGSSNSYAIKKKDEVERVAKANR ribosomal protein S7e Leishmania donovani 0.023867316 1 LEVO MQPYLRKLRKLKRGKPSDLEESVAKALFELETSHKTLRQELPRFHVNTVREVKVPRSKKTVLVVFYPLRFLMLVRKVQRA LTSELEKRHPGYLVMLVAQRKITKRPTDVYKLQKVQRSKTSTAVFENILNDMIYPSDVVGRRWRCRTDGSKLMKVFLDAR DRKRVESRLRAVAYVYKQLTHRRVSFGFMWNPKLQQVSTR E9B7A8 ribosomal protein S8 Leishmania donovani 0.014719257999999999 1 LEVO MTMMSVLANALRTIASAERRGKRQVLIRPSSKVVVKFLQVMQKHGYIGEFEIIDDHRAGKIVVNLNGRLNKCGAICPRFD CATTDYEKWMKNILPSRQFGFVVLTTSLGIMDHEEARSRNTGGKVLGFFY E9BAV6 ribosomal protein S8e Leishmania donovani 0.025038346 1 LEVO MGIVRSRLHKRKITGGKTKIHRKRMKAELGRLPANTRLGARRVSPVRARGGNFKIRALRLDTGNFAWASEAIAHRVRLLD VVYNATSNELVRTKTLVKNCIVAVDAAPFKRWYAKHYGIDLDADRKTTKAAAAAEKKGRKSVHAAADKYDVNKASPKLQR EWIRRRRNHRVEKAIADQLREGRVLARITSRPGQSGRADGILLEGAELQFYLKRLEKKKK E9BH78 ribosomal protein S9 Leishmania donovani 0.016718585999999997 1 LEVO MPADKSYALKQVQTFGKKKTAIAVATVTKAAQCNIKVNGVPLQQILPDTLRAKIMEAITVVGSKYYSRLRIDVAVHGGGQ VSQAYAARQAIAKGLIAFFQKYHNEVEKAALKDKFLAYDKFLLIADPRRCEPKKWGRHSARTRFTKSYR E9BI96 ribosomal protein S10 Leishmania donovani 0.013049075999999998 1 LEVO MDYPKKTQAAPAEGQTVRLTITSRNAKAVESVTSQLLMRARDEKVTIHGPVRLPTRTLKITTRKTPCGNGTNTWDTFELK IYKRIIDLHAPTEQVKKITSFTMESGVDVSITILDR ribosomal protein S10e Leishmania donovani 0.01743291 1 LEVO MWCARTRTGSHSHHPTQPGSPIDCAEAAPRRMSTYVPKPSRDNVYRFFFTEGVIACKKDRMGTWTGTLGGNTFTVPCIQV MQLMRSLKSRNLIKEQYAWRHYYWTLNDEGIAYMRSYLHLAPSAMPNTQKPSSVNFEKVTEGRGRGRGRGGRG E9BTG4 ribosomal protein S11 Leishmania donovani 0.015609087999999998 1 LEVO MSKKQEVKAYGPNVKKGDLVYGVVHIYASFNDTFVHVTDTSGRETYVKVTGGMKVKADRDESSPYAAMMAAQDVVARCKE CGINALHVKMRAVGGVRTKSPGPGAQAALRALARAGMKIGRIEDVTPIPTDSTRRKGSRRGRRL E9BMA8 ribosomal protein S12 Leishmania donovani 0.015952654 1 LEVO MTKTNGQNAARKLVRLRRRNRWADKGWKRAHTFAAKKANPFGGSSHAKGIVLEKIGVGAKQPNSAIRKCVRVQLIKNDKK IIAFVPNDGCLHFIEENDEVLVSGFGRSGHAVGDIPGVRFKIVKVSSVGLYALYRQKKEKPRN E9BFB6 ribosomal protein S12e Leishmania donovani 0.015611836999999998 1 LEVO MAEETVRVEVPAVEENVVVDVAPESLEDAVRIVIQKALEANGLVRGLSEVARTLDCKTAHMCILADDCEDEEYKKLVTAL AKQGNIDLINVEEREKLAQWAGLVRRDVAGEVTKTLKCSSVAIRDFGERTKALDYLLSQLH E9BBC0 ribosomal protein S13 Leishmania donovani 0.017443436 1 LEVO MSLTLIPDHFQHIVRLLNTNVEGKRKVPFALRMVKGVGIRFAYLVCKKAGIDVERRAGTLTAEELEKIAEIIADPAKFKI PDWFLNRQRDPKTGKTEHLSSSMVDTRLREDLERLKKIRAHRGVRHAYGLRVRGQHTCTTGRHGKTVGVSRGK E9BTF9 ribosomal protein S14 Leishmania donovani 0.006696929 1 LEVO MGHLDQWRSRQKIGMGKGARCCVICSNQKALIRKYELNVCRQCFRENAEHIGFTKLR E9BJV7 ribosomal protein S15 Leishmania donovani 0.01745574 1 LEVO MVRMHGNGRGKASSALPYRRTPPAWLKIASRNVVKMVCKSSRKGMMPSQIGMELRDSMGIAQVKNVTGRKILRILKHSGL APEIPEDLYFLVKRATQMRKHLERHTTDRDTKYRLILVESRIHRLARYYKRVKQLPPTWKYESSTASAMVA E9BPR7 ribosomal protein S17 Leishmania donovani 0.019985369 1 LEVO MSAAPQYYHAHQVDATIQHQKAYQRQTAVNENMHRSSRKHVNKSGHIRYAKKIGLGFKTPAKALNGKYIDRKCPFTSNVV IRGRILRGIVHSTKMHRTIVIRRNYLHFIKKYQRYQKRHKSLAVHCSPAFDPKQGDEVVVGQCRPLSKTIRYNVLEVVSK SAADKMGKKFAKN ribosomal protein S17e Leishmania donovani 0.016521465 1 LEVO MGKIRTKTVKRASRQVVEKYYSKLNFDFYQNKRVIMDVTIAESKKLKNKIAGYTTHIMKRLARGPVRGISLKLQEEERER RMDHAPATSDVDKAIQSGVSVDKRTMQMLQRLEIGVPRRVKRADAAVAKVKAAPRRRQQKSSK E9BJZ5 ribosomal protein S19 Leishmania donovani 0.017528462999999998 1 LEVO MASNITAERYEQLKKERTFHKFTYRGLEIDPLLALSEEEFRALVHARARRNMNRHVDRRPPVLLKRLREAKKHVKVGEKP KAVKTHLRDVVITPEMVGSVVAIYNGHQFNAVEIKGEMIGHYLGEFSMSYRPVLHGRPGVGATHSSRFIPIK ribosomal protein S19e Leishmania donovani 0.020188588 1 LEVO MYSPARMSFIRRVTNPSCIMAALKNKIHRIGKRKGASLKDVSAWRWIKTAARHFKQEGKIFVPNCTEIMKSSHGRERAPQ NPDWYYIRCAAVLRAIYLRPGVGYGGLSKRFGNKKNYGSRPEHTVTSSTGPLHWACKSLTKLGLVEPGAQSGQRLTRKGH KFADSLAFQVQIRKFGASK E9BR60 ribosomal protein S21e Leishmania donovani 0.016669115 1 LEVO MATIGMFNEEGENVDLYIPRKCHATNTLIEAHDHAAVQISIANVGPNGVINGTTTTLCIAGYLRSQGESDHAINHITIDR GIMRIKTGKPKRVSKSKSKKPTAGAAGQKGARPPAQKGARPSGQKGARPPAQKGARPPAQKGARPPAQKGAAPARKNRA ribosomal protein S24e Leishmania donovani 0.015808882 1 LEVO MVFQKKKAEVCIRTSQFKVNKLLNRKQFIVEVNHPHWCGTVPTQLIRKKLATLYKVPDASQVSLFGFKTKFGGGKTTGFG LIYDDLASLKRFEPNYRKTRMGFGKARLPARKSVKERRNRNKKLRGKAKGKQVAKKK E9BU11 ribosomal protein S25e Leishmania donovani 0.013071399 1 LEVO MPPKAGQTKKAKMEAANKGAKKTTKKWSKGQSREALQNAVMFDKETYDKLRSEVPKYKLITPSIISDRLKIAVSIAAAGL KQLCREKLIRLVSCSSKTRVYTRIVQAAPAEAAAAAPAAE E9BHM6 ribosomal protein S26e Leishmania donovani 0.012794251 1 LEVO MTTKRRNHGRSKPAHSRGRVKPIHCFNCGRLTPKDKAVGRFVVRRMLDAASARDVAEASPVYGANFPMPKLYMKQRFCIA CAIHSRTVRARPVGNRKIRYTRKVPFRPAGKK E9BK95 ribosomal protein S27e Leishmania donovani 0.009819462999999999 1 LEVO MGFFDADLSYPTVRTERMKHKRRRLVQGPNSYFMDVSCPRCRQVTVVYSHATTSVECKGCSKKLCRPTGGKALLVEGCGY RRKPDH E9BUA2 ribosomal protein S28e Leishmania donovani 0.009763191000000001 1 LEVO MADSKKDNKKTEEVVTQGTDQAQVGLIIKVLGRTGSRGNVTQVRVRLMAEAGSPDYNRTIVRNVKGPCKENDMLSLMETE REARRLR E9BIH3 ribosomal protein S30e Leishmania donovani 0.007394894 1 LEVO MGKIHGSLARAGKVKNQTPKVAKQEKPKQPRGRALKRLKYTRRFLSKTVKPGEKVHMNKQPPGKAG E9BLG3 ribosomal protein S31e Leishmania donovani 0.017015726999999998 1 LEVO MQIFIKNAAGRSVAVRVSAEDTVASLKAQANVTQGNLFFAGMCLAEEETLAAYGLSKESTVDVVIPVEGGKGKKKKKRIF TKPKKPTHRHKLEKMRALKYFKVTENDDGSYKVERTRQDCPHPQCGAGVYMAQHKDRQYCGKCHLTYKAESK E9BTC5 LACK1 Leishmania donovani 0.034459523 1 LEVO MNYEGHLRGHRGWVTSLACPEQAESYIKVVSTSRDGTAIAWKANADRHSVDSDYGLPSHRLEGHTGFVSCVSLAHATDYA LTASWDRSIRMWDLRNGQSQRKFLKHTKDVLAVAFSPDDRLIVSAGRDNVVRVWNVAGDCMHEFLRDGHKDWVSSICFSP SLEHPIVVSGSWDNTIKVWNVNGGKCERTLKGHSNYVSTVTVSPDGSLCASGGKDGVALLWDLSTGEQLFKINVESPINQ IAFSPNRFWMCVATEKSLSVYDLESKTVIAELTPDGAKPSECISIAWSADGNTLYSGHKDNLIRVWSISDAE Q9BIJ5 ribosomal RNA 18S Leishmania donovani 0.7102874379999999 1 GAUCUGG(OMU)UGAUUCUGC(OMC)AGUAGUCAU(A2M)UGCU(OMU)GUUU(OMC)AAGGACUUAGCCAUGCAUGCCU CAGAAUCACUGCAUUUGCAGGAAUCUGCGCAUGGCUC(A2M)UUACAUCAGACGUAAU(OMC)UGCCGCAAAAAUCUUGC GGUUUCCGCAAAAUUGGAUAACUUGGCGAAACGCCAAGCUAAUACAUGAACCAACCGGGUGUUCUCCACUCCAGACGGUG GGCAACCAUCGUCGUGAGACGCCCAGCGAAUGAAUGACAGUAAAACCAAUGCCUUCACUGGCAGUAACACCCAGCAGUGU UGACUCAAUUCAUUCCGUGCGAAAGCCGGCUUGUUCCGGCGUCUUUUGACGAACAACUGCCCUAUCAGCUGGUGAUGGCC GUGUAGUGGACUGCCAUGGCGUUGACGGGAGCGGGGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUAGCUACC ACUUCUACGGAGGGCAGCAGGCGCGC(A2M)AAUUGCCCAAUGUCAAAACAAAACGAUGA(OMG)GCAGCGAAAAGAAAU AGAGUUGUCAGUCCAUUUGGAUUGUCAUUUCAAUGGGGGAUAUUUAAACCCAUCCAAUAUCGAGUAACAAUUGGAGGACA AGUCUGGUGCCAGCACCCGCGGUAAUUCCAGCUCCAAAAGCGUAUAUUAAUGCUGU(OMU)GCUGUU(A2M)AAGGGUUC GUAGUUGAACUGUGGGCUGUGCAGGUUUGUUCCUGGUCGUCCCGUCCAUGUCGGAUUUGGUGACCCAGGCCCUUGCAGCC CGUGAACAUUCAAAGAAACAAGAAACACGGGAGUGGUUCCUUUCCUGAUUUACGCAUGUCAUGCAUGCCAGGGGGCGUCC GUGAUUUUUUACUGUGACUAAAGAAGCGUGACUAAAGCAGUCAUUUGACUUGAAUUAGAAAGCAUGGGAUAACAA(A2M) GGAGCAGCCUCUAGGCUACCGUUUCGGCUUUUGUUGGUUUUAAAGGUCUAUUGGAGAUUAUGGAGCUGUGCGACAAGUGC UUUCCCAUCGCAACCUCGGUUCGGUGUGUGGCGCCUUUGAGGGGUUUAGUGCGUCCGGUACGAGCUCCGGUUCGUCCGGC CGUAACGCCUUUUCAACUCACGGCCUCUAGGAAUGAAGGAGGGUAGUUCGGGGGAGAACGUACUGGGGCGUCAGAGGUGA AAUUCUUAGACCGCACCAAGACGAACUACAGCGAAGGCAUUCUUCAAGGAUACCUUCCUCAAUCAAGAACCAAAGUGUGG AGAUCGAAGAUGAUUAGAGACCAUUGUAGUCCACACUGCAAACGAUGACACCCAUGAAUUGGGGAUCUUAUGGGCCGGCC UGCGGCAGGGUUUACCCUGUGUCAGCACCGCGCCCGCUUUUACCACCUUACGUAUCUUUUCUAUUCGGCCUUUACCGGCC ACCCACGGGAAUAUCCUCAGCACGUUUUCUGUUUUUUCACGCGAAAGCUUUGAGGUUACAGUCUCAGGGGG(OMG)AGUA CGUUCGCAA(OMG)AGUGAAACUUAAAGAAAUUGACGGAAUGGCACCACAAGACGUGGAGCGUGCGGUUUAAUU(M1Y)G AC(C4J)(5MC)AACAC(OMG)GGGAACUUUACCAGAUCCGGACAGGAUGAGGAUUGACAGAUUGAGUGUUCUUUCUCGA UUCCCUGAAUGG(OMU)G(OMG)UGCAUGGCCGCUUUUGGUCGGUG(OMG)AGUGAUUUGUUUGGUUGAUUCCGUCAACG GACGAGAUCCAAGCUGCCCAGUAGAAUUCAGAAUUGCCCAUAGGAUAGCAAACUCAUCGGCGGGUUUUACCCAACGGUGG GCCGCAUUCGGUCGAAUUCU(OMU)CUCUGCGGGAUUCCUUUGUAAUUGCACAAGGUGAAAUUUUGGGCAACAGCA (OMG)GUC(OMU)GUGAUGCUCCUCAAUGUUCUGGGCGACACGC(OMG)(OMC)ACUACAAUGUCAGUGAGAACAAGAAA AACGACUUUUGUCGAACCUACUUGAUCAAAAGAGUGGGGAAACCCCGGAAUCACAUAGACUCACUUGGGACCGAGGAUUG CAAUUA(OMU)UGGUCGCGCAACGAG(7MG)AAUGUCUCGUAGGCGCAGCUCAUCA(A2M)ACUGUGCCGAUUACGUCCC UGCCAUU(OMU)GUACACACCG(4OC)C(5MC)GUCGUUGUUUCCGAUGAUGGUGCAAUACAGGUGAUCGGACAGGCGGU GUUUUAUCCGCCCGAAAGUUCACCGAUAUUU(OMC)UUCAAUAGAG(OMG)AAGCAAAAGUCGUAACAAGGUAGCUGUAG GUG(MA6)(MA6)CCUGCAGCUGGAUCAUUU FR799614.1 tRNA-Phe Escherichia coli 0.024599747999999998 1 GCGCGGAUAGCUCAGUCGGUAGAGCAGGGGAUUGAA(MIA)AUCCCCGUGUCCUUGGUUCGAUUCCGAGUCCGCGCACCA CP022229.1 P-site tRNA Escherichia coli 0.024786785 1 CGCGGGGUGGAGCAGCCUGGUAGCUCGUCGGGCUCAUAACCCGAAGAUCGUCGGUUCAAAUCCGGCCCCCGCAACCA CP011320.1 E-site tRNA Escherichia coli 0.024485539 1 GCGCGGAUAGCUCAGUCGGUAGAGCAGGGGAUUGAAAAUCCCCGUGUCCUUGGUUCGAUUCCGAGUCCGCGCACCA CP022229.1 mRNA Leishmania donovani 0.004085501 1 CACCAUGUUCAAA MAGNESIUM ION 2.4305e-05 24 MG PAROMOMYCIN 0.000615628 6 PAR water 1.8015e-05 262 HOH singleParticle particle 7.6 ETHANE FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K2 SUMMIT (4k x 4k) 1.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 2.7 FSC 0.143 CUT-OFF 141028 PROJECTION MATCHING PROJECTION MATCHING