6AZ3
Cryo-em structure of of the large subunit of leishmania ribosome bound to paromomycin
PDB DOI: 10.2210/pdb6az3/pdb
Classification: RIBOSOME/ANTIBIOTIC Organism(s): Leishmania Donovani
Deposited: 2017-09-09 Deposition Author(s): Bashan, A. , Isobe, T. , Jaffe, C.L. , Matzov, D. , Nobe, Y. , Rozenberg, H. , Shalev-Benami, M. , Skiniotis, G. , Taoka, M. , Yonath, A. , Zhang, Y. , Zimmerman, E.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 2.5 Å
Cryo-em structure of of the large subunit of leishmania ribosome bound to paromomycin
Bashan, A. , Isobe, T. , Jaffe, C.L. , Matzov, D. , Nobe, Y. , Rozenberg, H. , Shalev-Benami, M. , Skiniotis, G. , Taoka, M. , Yonath, A. , Zhang, Y. , Zimmerman, E.
Primary Citation of Related Structures: 6AZ3
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 60S_ribosomal_protein_L35_putative/GeneDB:LmjF.26.2330/GeneDB:LmjF.26.2340 | A | 125 | Leishmania Donovani | SHHMKIKDLREKSKDDLLKTLTEYKKELSQLRVVQQTGGAETRLGRIRPIRKSIARILTVLNQNERSNLKMFYADRKLRCKTPKVLRAKLTHRRRLALKENEKNRKTSRQMRQAHKFPKRVYAVK |
| 60S ribosomal protein L37 | J | 80 | Leishmania Donovani | TKGTTSMGQRHGRTHILCRRCGRNSYHVQWERCAACAYPRASRRRYNWSVKAIKRRRTGTGRCRYLKVVNRRIANHFKTP |
| Ribosomal L38e family protein | K | 76 | Leishmania Donovani | PREIKTLKEFLAICSRKDARCVKVKHNPSATKFKVRCSRYLYTLVVNDKKKADKIERSIHPSVKKIAVTARSHAKT |
| 60S ribosomal protein L39, putative | L | 50 | Leishmania Donovani | GRFKPLAVKKKYAKKMNQNKPVPYWIRLRTGNRIKWNEKRRHWRRTKLNY |
| Ubiquitin-60S ribosomal protein L40 | M | 50 | Leishmania Donovani | MEPTLVALAKKYNWEKKVCRRCYARLPVRATNCRKKACGHCSNLRMKKKL |
| ribosomal protein eL41 | N | 33 | Leishmania Donovani | GTVSRPRGMRPKWHKKRIKRLKLRRRRMRQRSK |
| 60S ribosomal protein L37a | O | 90 | Leishmania Donovani | AKRTVKMGVMGRYGTRYGANPRKRAKKLEVSQHAKHFCSFCGKFAFRRKAVGIWRCDGCSKTVAGGAYTLSTPNNSTVRSTVRRLRELAK |
| 60S ribosomal protein L44, putative | P | 96 | Leishmania Donovani | VNYPKKKVMHCGDARCNAHKSFKVVQYKAGKARLFARGKRRYDRKQSGYGGQTKPVFHKKAKTTKKIVLKLQCSGCKSIRQVVLKRTKHFELNDKK |
| Ribosomal protein L19e family protein | Q | 189 | Leishmania Donovani | VSLKLQARLASSILGCGRARVWLDPNEAVEIQNANSRKSVRKLIKDGFIIRKPVKVHSRARWRKMKEAKDMGRHNGVGRREGSREARMPSKELWMRRLRILRRLLRKYRADKKIDRHVYRDLYVRAKGNVFRNKRNLVEHIHKIKNEKKKERQLAEQLAAKHLRDEQNRNKARKQELRKREKERERARR |
| 60S ribosomal protein L18a | R | 178 | Leishmania Donovani | VKPHLRHYQVVGRESPSEKNPEPTVYKFEVFAPNFVVAKSRFWRMMRVKNKVKATHGDVLSCKVVKDAKLVARNYLVDIAYYSQRCGYTRMVKEFRDVSKTGAVSQAYHDLASRHRARYHNIEVLNVKSIPDHEVKHLSIAQYHAPNLSFPLLQRRIKAARKDRAIFVKKNTKRAVVA |
| 60S ribosomal protein L21, putative | S | 154 | Leishmania Donovani | VHSYGYKSGTRHLFAKKFRKHGAPSVSTILTNIKVGDYVDVVADSAVREGMPHKYYHGRTGIVWNVTPRGVGVIINKPVRTRTLRKRICVRFEHVRKSRCQEAFKAKEHQFQAYLAAKKAGKALPPLKKSSRMGGIVRPKNVEVLARRVADYEA |
| 60S ribosomal protein L29 | B | 68 | Leishmania Donovani | AKSKNHTNHNQSSKNHRNGIKGPMPLHLHNSKRGSWLPALVNARRVRKHNQKAALKKRRERIAAFAAK |
| 60S ribosomal protein L17, putative | T | 154 | Leishmania Donovani | THYSRKPQVSSKSAKAKVSDLRCHYKNTFETANVINGMPLRKAQQLYRQVLAKTRCIPFKRYNGKIGRTAQAKEWGQTKGRWPRKSVVAMMSLLKNAEANAIEKGLDPNQMVIKHVQVDQAARMRRRTYRAHGRITPYMCSPCHVQLFMSEKKE |
| 60S ribosomal protein L22, putative | U | 121 | Leishmania Donovani | VAVRAKVGSRSYVRQKQLAKGKKVFKIDCSIPAADGIFSEDVLGNFEQFFQDNTKLNGRKGKLSDKVRLSMNDNVLTISTTMAYRKKYFKYLTKKFLKKKDLRDWIRILATGKGTYQLKYF |
| 60S ribosomal protein L23a, putative | V | 118 | Leishmania Donovani | AKSYTRPQFRRPHTYRKPAMAKPSNRVTVESKDIAAFSVIRYPLTTDKAMKKIEENNTLTFIVDSRANKTEIKKAMRKLYQVKAVKVNTLIRPDGLKKAYIRLSAAHDALDTANKIGL |
| ribosomal protein uL24 | W | 121 | Leishmania Donovani | ASIKCGSRRKARRAHFQAPSHVRRVLMSAPLSKELRAKYNVRAMPVRKDDEVIVKRGTFKGREGKVTACYRLKWVILIDKVNREKANGSTVAVGIHPSNVEITKLKLTHHRKSILERKDRS |
| ribosomal protein eL24 | X | 65 | Leishmania Donovani | MRTIECEFSHFAVHPGHGRRYVPFAFLSTKPVLTFSRPKCFALYMRKKNPRFIPWTRTYRRIHRK |
| Ribosomal L27e family protein | Y | 132 | Leishmania Donovani | KFLKPGKVVIVTAGRYAGHKAVIVQNSDIATKERPYGRALLAGIKKYPKKVVRGMSKQTIARRSQVGVFLRVVNHKHFLPTRYNVDMSKELRGKINVSDASKRSRSKRLVRHVFQARYNAGSSMWFFQRLRF |
| 60S ribosomal protein L28, putative | Z | 140 | Leishmania Donovani | SHSVDLQWILVRQNSRFLQKRGGIRMSNDPFNNNGNWTKRHCGFLNEKAAVVKPAKGGAICVTVKDGSSNNKPRQTYRKTVHAAGVRASDVSRAVAAVRPDLADVSFRRARRMACIASRTAKVAAARKARSEKIKFSRKS |
| Ribosomal protein L1a, putative | C | 366 | Leishmania Donovani | RPSVSVYSASSDSVVGTCPLPAVFTAPIRNDIVKFVHTNMAKNSRQAYAVNRLSGMNHSAHSWGTGRAVARIPRISGGGTSTSGAGAFGNMCRGGRMFAPTKIFRRWHRKINLHQKRFAVVSALAASSVPSLVMSRGHRIDNVPEVPLVVEDSIQGYEKTKEAMAFLKAIAAIDDVNRVNDSREIRAGRGKMRNRRYVARRGPMLVMPNNKGTRAFRNIFGLDLANVSALNLLHLAPGGHVGRFVIWTKSAFEQLDKIFGTFTEASAVKKGFTLPAPMLTNTDVTRIMQSEEVRRVLKPKKLQAKKASRYQTPTNGIKNRRLRLRLNPYVKRETAAAKGMRNVANRDARRKAKMARVTKAKKAATK |
| 60S ribosomal protein L11 (L5, L16) | D | 168 | Leishmania Donovani | ANPMREIVVKKLCINICVGESGDRLTRASKVLEQLCEQTPVLSRARLTVRTFGIRRNEKIAVHCTVRGKKAEELLEKGLKVKEFELKSYNFSDTGSFGFGIDEHIDLGIKYDPSTGIYGMDFYVVLGRRGERVAHRKRKCSRVGHSHHVTKEEAMKWFEKVHDGIIFQ |
| 60S ribosomal protein L9, putative | E | 186 | Leishmania Donovani | VKVKSLCTLQIPEGVTVDVKGRKVTVTGKRGTLTKDLTHLQLDLRVDKKNRTFTVIRWFGSKIPIACLNTTKAHVQNMITGVTKGYRFKVRCAYAHFPINVSVDGQNIEVRNFLGEKRVRRQLVPSSVKVSQTDPSKVKDEIIFDGNDLEQVSREAAVLHQMCLVKKKDIRKFLDGIYVQTKTNIE |
| ribosomal protein eL6 | F | 195 | Leishmania Donovani | MAATKSAASAAKRKAAKKVSRKSPEYTTLRKSCAPGVIAIILAGRFRGRRAVILKQLPHNGPLVVSGPMKYNGVPIRRIDSRYVIATSTKVDISSVDTAPITPEVFQRPKAEKLTKSEGDFMGDKQKARAEKAAKKTSKAGKKTPVSDARAQLQKKIDAALIAAIKKDAQGKEKAGYLRSVFTVKPGDAPHRWNW |
| 60S ribosomal protein L7a | G | 348 | Leishmania Donovani | MTVRSSPTANLYLTYLLLSCPICTSPFPFATLIRTHLHHRVAPAFAFLLFFGCAHVCACVLARLLLPYFHSTFSASISRRAEKSMPGKEVKKATQPAKAASPYKKPAVASHFAARPKNFGIGQDVPYARDLSRFMRWPTFVTMQRKKRVLQRRLKVPPALNQFTKVLDRASRNEALKLIKKYAPETRKARRERLHKAAEEKKKDPKKTVSTRAPLAVVTGLQEVTRAIEKKQARMVVIANNVDPVELVLWMPNLCRANKIPYAIVKDMARLGDAIGRKTATCVAITDVNAEDEATLKNLIRSVNARFLSRSDVIRRQWGGLQLSLRSRAELRKKHARNAGVDAAAIIQ |
| ribosomal protein uL13 | H | 221 | Leishmania Donovani | AFPSRKDASRAQRKSAKKHRPEIIVIDLKDHVLGRAAAVVAKQLLLGKKITVVRCEQLNIAGTEIRNKIKYLQYLRKRKLTNPTKGPFHHRAPSDVFVRTVRSMLPRYTKRGMKALNSLVAYEGIPPNVVRTGGRVVIPRAQRHVCYRSERPYTVLGNMCKHVGWKYSDVVANLEKARVEKASRHHEKQAKLREAWKAARKEALAKMPKHNVEVLKKFGYA |
| ribosomal protein eL13 | I | 212 | Leishmania Donovani | PKGNNAIPHVHQKKHWNPCSSQKGNVKVFLNQPAQKHRRRRLRLLKAKKVFPRPLKALRPQVNCPTVRHNMKRRLGRGFSPAELKAAGLNPQYAATIGIRVDSRRKNKSEEGMNVNVQRLKTYMSKLVLFPMNHKKVQKGEASEEEVKAATQDRSRFGDAAVGAVVYPSAETPRAVSAEEKSMCVYAFLKKNHSAVRFFGARSARAARKEAA |
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| rRNA alpha | 1 | 1778 | NA | AGACCUGAGUGUGGCAGGACUACCCGCCGAACUUAAGCAUAUUACUCAGCGGAGGAAAAGAAAACAACCGUGAUUCUCUCAGUGAGCGGCGAGCGAAGAGGGAACGAACUCGUUGCCGAAUCGGGUCUUACAAGGCCUUGAGUUGUGGCACAAAUAUCAUUUCGUGGUUGGUGCAGGAGUGGCGAAAUUCAAGCGCAAAGCAAACCCGUUGCUGAAUACAACCCUUCAUGUGAGUAUUGAGCCAAAGAAGGUGUUAGCCCAUUGAGCCAUAAACCUGAGCGCCUCAUGAACUGUAUUAAGCGAGUAGCACUGUUUGGGAAUGCAGUGUCAAGUUGGCAGGUAUUUGUCUGCCAAAGUUAAAUACAGAGUAGGAAGACCGAUAGCGAACAAGUAGCGUGAGCGAAAGUUUGAAAAGCACUUUGGAAAGAGAGUGAAAUAGAACCUGAAGUCGUGACAAAGACAAUGGAAGUACCUCCAUUUCAACGGCCAGAACCAGCCCUACUGCAUUAUCCUGUCGGGGGUCAAAAUCCGGCGGGCAACGAAGUGCAAGAAUUUUGGGUCUUGGUGAAAUGAGCGGAGUAUUUGAGCUGUGCACGGCGCAAGCCGCACGCACUGGUUUCUUCUCCGUGAUGCUCCAUGUUGGCGAUGGAAAUGGGGUGCCCCCACCCGUCUUGAAACACGGACCAAGGAGUCAAACAGACGCGCAAGGGAGGAGAUAUGGUUGCCAGUACUUCUCUCGUACUGAAAGGGAGAUGCAAAAUGCAUCUGUGGUGUGCACACGUCAAAUCCGUUUGAUUUGCCCAACACCGACCGGCCCUCCGUGGGUUGCGUUGGAGUGUGCCUGUUUGGACCCGAAAGGUGGUGAACUAUGCCUGAACAAGGUGAAGCCCGGGGAAACCCAGGUGGAGGCCUGUAGCGAUGCUGACGUGCAAAUCGCUCGUAUGAUUUGGGUAUCGGAGCGAAAGACUCAUCGAACCACCUAGUAGCUGGUUCACAUCGAAGUUUCCCUCAGGAUAGCUGGUGCUAGUAGAAGUAUUGUGCGGUAAAGCAAAUGAUUAGAGGCAUUGGUGUUCUUAGAAUAUCGACCUAUUCUCAAACUUUAAAUGUGCAAACAAACCGUGCCUUAGCCAACUGCAAGGCCGGAAAGAAAAGAAUUAGAGGCACCAAGUGGGCCUUCUUCGGUAAGCGGAGCAGGCGAUGCGGAAUGAACCGCUUAGGGAUAUGUGGCGUCAAAACUUAUGGGCUCAUUCUCGAUACGUGAAAAGGGUGUUGGUGGAUUGGACAGUUGGACGGUGGCCAUGGAAGUCGGCAUCCGCUAAGGAGUGUGUAACAACUCACCAACCGAAUCCACCGGCCCCGAAAAUGGAUGACGCUUAAGCCCAAUUAGUGAUUGCCCAUUAUUCCUUUGGUAAGGGCGGAAACAAACUCUUGGAGAAAGUGUAGCCCUUCCGAUGUAGAUGUGGCCUGGAGGUUAGGACGAAGCUUAUGGCGUGAGCCUAAGAUGGACCGGCCUCUAGUGCAGAUCUUGGUUGGCGUAGCAAAGAUCUAACGGAGAUAUACUCAACAUGCAACGUUGGAUACUGGAGCGGGGAAGGAUUUCGUGCCAACGGCACUCGUACACGAGUUGUUCGGAAACUGAGCACAACGUUAUAUCGUUUUGUUAGGAAAGUGAAGGUGUGUCGGCGGCAGCUGCUUUCGGGUAGCUGUUCGACUGGCCAUAACUGAAAAGGGGCAACAGAGAACCUGGGAUUAUAUUCCAAAAAGAAAUUGCAUGUGGG |
| rRNA beta | 2 | 1526 | NA | CCCAACUGCAGACCGUACUCAUCACCGCAUCAGGUCCCCAAGCAUAGAAUGCUCUGGUACAUAGAGAAAGGUACACUCAGGGAAGUCGGCAAAAUAGAUGCGUAAGUUCGCAAGAAGCAUUGGCUCUGAGGGCAAAGUCAGAGAAAACCGGAAGGCCAGUGUCCUCUCGCAUGCAGCCGUUCUUCAGAUGUUGUUUUGGCGCUCGCCGCCUUAGCACGCUGAUAGCGACUGUACUGUCGUCUGUGAAGGCUACCUUCCCGAGGCGUCGUAACCCGGCGUCUCACUCUGGCACGGGCCGGUCUUGGCGGGUUCACGCUCGCCUUGUGCCGCGUCCCACAAAUUGCCAACUCAGAACUGCUUACGGCGGGGAAUCCAACUGUAUAAUUAAAACAUAGGUUUGUGAUGCAUCCAAGUGGUGUAUAUCGCAAACUGAUUUCUGCCCAGUGCUCUGAAUGUCAACGUGACGAGAUUCACCGACGCGCGGGUAAACGGCGGGAGUAACUAUGACUCUCUUAAGGUAGCCAAAUGCCUCGUCUUCCAAUUAGAGACGCGCAUGAAUGGAUUAAUGAGAUUCCCUCUGUCCCGAGUUACUAUCUAGCGAAACGACAGUCAAGGGAACGGACUUGAAGGGCUAAGCGGGGAAAGAAGACCCUGUUGAGUUUGACUCCAGUCUGGCUCUGUGCGGCGACAUCUGAGGUGUAGUAUAGGUGGAAGCGCAAGCGCAAAUGAAAUACCACCACUCGGAACGUUGCUUCACUUAUCGAAUGAAGAGACCAAUGGGUUUAGCGUAGUCUUCGGGCUAUGCACCGUCUAGGUUUGGGAGUAAUUUUAUGGCGGUAACCCCGUCCCCACGGGAAAGGGUGGUGUGCUUUUUUCUGCGUGCGUCUUCACGGGCGUCGCGCGGGCCCCGCUCUUUUUUAUUACGUUUCCUUCGGGGGGCGUGACUCGUGGGUACCCAACCGUGCUGUAAACUGAACCAACGGGAUUGCCUCGUGCAGUUCCGGAGUCUUGUUUCGAGACAUCUGCCAGAUGGGGAGUUUGGCUGGGGCGGCAUAUCUGUUACACGACAACGCAGGUGUCCUAAGGCGAGCUCAGUGGGAACAGAAAUCUCACGUAGAACACAAGCGUAAAAGCUUGCUUGAUUAACGAUUUCCAGUACGAAUCGAGACUGCGAAAGCAAGGCCAGCGAUCCUUUGCGAAGAAUAGGAAAUAUGAACAAAUCAUACCAGAGGUGUCAGAAUAAUUACCACAGGGAUAACUGGCUUGUGGCGGCCAAGCGUUCAUAGCGACGUCGCUUUUUGAUCCUUCGAUGUCGGCUCUUCCUAACCUAGCGCCGCAGAAGACGCUAAGGGUUGGAUUGUUCACCCACUGACAGGGAACGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUUGGUUUUACCCUACUUAGCUGGAAAUUGCGAGAAAAAGAUUAUCCGUGCAAAGCGGACGUCGGGUCGUUCUUGGGCCUGGCGAGCGGUGGGUAGUACUUGGUACGCUCAUCACC |
| rRNA gamma | 3 | 211 | NA | AGUGGUAAUGCGAAACACUGCCAGGUAACAAAUCAAUCCUCCCACGGUGAGCUUUCUUUUCACCAUAAUCCACAUCUCCGGCUUUGCUGGGGCUUGGGCCUUUUUACUUCUCGCGUUGUUCGGAGCGGGGGCUCAAGAUUGAAAAAUGCAGCUCUCCCUACGUACUGUCAUUGUUGUGAGUUCUGCGCAUUAACGCAAAAACCUGGGGUGU |
| rRNA delta | 4 | 183 | NA | GUGAGAUUGUGAAGGGAUCUCGCAGGUAUCGUGAGGGAAGUAUGGGGUAGUACGAGAGGAACUCCCAUGCCGUGCCUCUAGUUUCUGGGGUUUGUCGAACGGCAAGUGCCCCGAAGCCAUCGCACGGUGGUUCUCGGCUGAACGCCUCUAAGCCAGAAGCCAAUCCCAAGACCAGAUGCCCAC |
| rRNA epsilon | 5 | 133 | NA | UACGUCCCUCUCCAAACGAGAGAACAUGCAUGGGCUGGCAUGAGCGGCAUGCUUCACUUCGGUGGGGCUCGAGGGGCAUUUACGUCCCGAGGCGCUGAACCUUGAGGCCUGAAAUUUCAUGCUCAGGGACACA |
| rRNA zeta | 6 | 71 | NA | AUCGAAUCGCCACCUACAAGACUGGAGCUUGCUCCCUCGAAGGCGCCAAGUAUAUUCAUGAUCACAAGACA |
| rRNA 5.8S | 7 | 171 | NA | AACGUGUCGCGAUGGAUGACUUGGCUUCCUAUUUCGUUGAAGAACGCAGUAAAGUGCGAUAAGUGGUAUCAAUUGCAGAAUCAUUCAAUUACCGAAUCUUUGAACGCAAACGGCGCAUGGGAGAAGCUCUAUUGUGUCAUCCCCGUGCAUGCCAUAUUCUCAGUGUCGAAC |
| rRNA 5S | 8 | 118 | NA | GAGUACGACCAUACUUGAGUGAAAACACCAUAUCCCGUCCGAUUUGUGAAGUUAAGCACUCACAGGCUCAGUUAGUACUGAGGUCAGUGAUGACUCGGGAACCCUGAGUGCCGUACUC |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2017-09-09 Deposition Author(s): Bashan, A. , Isobe, T. , Jaffe, C.L. , Matzov, D. , Nobe, Y. , Rozenberg, H. , Shalev-Benami, M. , Skiniotis, G. , Taoka, M. , Yonath, A. , Zhang, Y. , Zimmerman, E.