3JCS
2.8 angstrom cryo-em structure of the large ribosomal subunit from the eukaryotic parasite leishmania
PDB DOI: 10.2210/pdb3jcs/pdb
Classification: RIBOSOME Organism(s): Leishmania Donovani
Deposited: 2016-01-21 Deposition Author(s): Bashan, A. , Halfon, Y. , Jaffe, C.L. , Matzov, D. , Rozenberg, H. , Shalev-Benami, M. , Skiniotis, G. , Yonath, A. , Zackay, A. , Zhang, Y. , Zimmerman, E.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 2.8 Å
2.8 angstrom cryo-em structure of the large ribosomal subunit from the eukaryotic parasite leishmania
Bashan, A. , Halfon, Y. , Jaffe, C.L. , Matzov, D. , Rozenberg, H. , Shalev-Benami, M. , Skiniotis, G. , Yonath, A. , Zackay, A. , Zhang, Y. , Zimmerman, E.
Primary Citation of Related Structures: 3JCS
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 26S alpha ribosomal RNA | 1 | 1782 | NA | ACAGACCUGAGUGUGGCAGGACUACCCGCCGAACUUAAGCAUAUUACUCAGCGGAGGAAAAGAAAACAACCGUGAUUCUCUCAGUGAGCGGCGAGCGAAGAGGGAACGAACUCGUUGCCGAAUCGGGUCUUACAAGGCCUUGAGUUGUGGCACAAAUAUCAUUUCGUGGUUGGUGCAGGAGUGGCGAAAUUCAAGCGCAAAGCAAACCCGUUGCUGAAUACAACCCUUCAUGUGAGUAUUGAGCCAAAGAAGGUGUUAGCCCAUUGAGCCAUAAACCUGAGCGCCUCAUGAACUGUAUUAAGCGAGUAGCACUGUUUGGGAAUGCAGUGUCAAGUUGGCAGGUAUUUGUCUGCCAAAGUUAAAUACAGAGUAGGAAGACCGAUAGCGAACAAGUAGCGUGAGCGAAAGUUUGAAAAGCACUUUGGAAAGAGAGUGAAAUAGAACCUGAAGUCGUGACAAAGACAAUGGAAGUACCUCCAUUUCAACGGCCAGAACCAGCCCUACUGCAUUAUCCUGUCGGGGGUCAAAAUCCGGCGGGCAACGAAGUGCAAGAAUUUUGGGUCUUGGUGAAAUGAGCGGAGUAUUUGAGCUGUGCACGGCGCAAGCCGCACGCACUGGUUUCUUCUCCGUGAUGCUCCAUGUUGGCGAUGGAAAUGGGGUGCCCCCACCCGUCUUGAAACACGGACCAAGGAGUCAAACAGACGCGCAAGGGAGGAGAUAUGGUUGCCAGUACUUCUCUCGUACUGAAAGGGAGAUGCAAAAUGCAUCUGUGGUGUGCACACGUCAAAUCCGUUUGAUUUGCCCAACACCGACCGGCCCUCCGUGGGUUGCGUUGGAGUGUGCCUGUUUGGACCCGAAAGGUGGUGAACUAUGCCUGAACAAGGUGAAGCCCGGGGAAACCCAGGUGGAGGCCUGUAGCGAUGCUGACGUGCAAAUCGCUCGUAUGAUUUGGGUAUCGGAGCGAAAGACUCAUCGAACCACCUAGUAGCUGGUUCACAUCGAAGUUUCCCUCAGGAUAGCUGGUGCUAGUAGAAGUAUUGUGCGGUAAAGCAAAUGAUUAGAGGCAUUGGUGUUCUUAGAAUAUCGACCUAUUCUCAAACUUUAAAUGUGCAAACAAACCGUGCCUUAGCCAACUGCAAGGCCGGAAAGAAAAGAAUUAGAGGCACCAAGUGGGCCUUCUUCGGUAAGCGGAGCAGGCGAUGCGGAAUGAACCGCUUAGGGAUAUGUGGCGUCAAAACUUAUGGGCUCAUUCUCGAUACGUGAAAAGGGUGUUGGUGGAUAUGGACAGUUGGACGGUGGCCAUGGAAGUCGGCAUCCGCUAAGGAGUGUGUAACAACUCACCAACCGAAUCCACCGGCCCCGAAAAUGGAUGACGCUUAAGCCCAAUUAGUGAUUGCCCAUUAUUCCUUUGGUAAGGGCGGAAACAAAACUCUUGGAGAAAGUGUAGCCCUUCCGAUGUAGAUGUGGCCUGGAGGUUAGGACGAAGCUUAUGGCGUGAGCCUAAGAUGGACCGGCCUCUAGUGCAGAUCUUGGUUGGCGUAGCAAAGAUCUAACGGAGAUAUACUCAACAUGCAACGUUGGAUACUGGAGCGGGGAAGGAUUUCGUGCCAACGGCACUCGUACACGAGUUGUUCGGAAACUGAGCACAACGUUAUAUCGUUUUGUUAGGAAAGUGAAGGUGUGUCGGCGGCAGCUGCUUUCGGGUAGCUGUUCGACUGGCCAUAACUGAAAAGGGGCAACAGAGAACCUGGGAUUAUAUUCCAAAAAGAAAUUGCAUGUGGG |
| 26S delta ribosomal RNA | 2 | 1527 | NA | UCCCAACUGCAGACCGUACUCAUCACCGCAUCAGGUCCCCAAGCAUAGAAUGCUCUGGUACAUAGAGAAAGGUACACUCAGGGAAGUCGGCAAAAUAGAUGCGUAAGUUCGCAAGAAGCAUUGGCUCUGAGGGCAAAGUCAGAGAAAACCGGAAGGCCAGUGUCCUCUCGCAUGCAGCCGUUCUUCAGAUGUUGUUUUGGCGCUCGCCGCCUUAGCACGCUGAUAGCGACUGUACUGUCGUCUGUGAAGGCUACCUUCCCGAGGCGUCGUAACCCGGCGUCUCACUCUGGCACGGGCCGGUCUUGGCGGGUUCACGCUCGCCUUGUGCCGCGUCCCACAAAUUGCCAACUCAGAACUGCUUACGGCGGGGAAUCCAACUGUAUAAUUAAAACAUAGGUUUGUGAUGCAUCCAAGUGGUGUAUAUCGCAAACUGAUUUCUGCCCAGUGCUCUGAAUGUCAACGUGACGAGAUUCACCGACGCGCGGGUAAACGGCGGGAGUAACUAUGACUCUCUUAAGGUAGCCAAAUGCCUCGUCUUCCAAUUAGAGACGCGCAUGAAUGGAUUAAUGAGAUUCCCUCUGUCCCGAGUUACUAUCUAGCGAAACGACAGUCAAGGGAACGGACUUGAAGGGCUAAGCGGGGAAAGAAGACCCUGUUGAGUUUGACUCCAGUCUGGCUCUGUGCGGCGACAUCUGAGGUGUAGUAUAGGUGGAAGCGCAAGCGCAAAUGAAAUACCACCACUCGGAACGUUGCUUCACUUAUCGAAUGAAGAGACCAAUGGGUUUAGCGUAGUCUUCGGGCUAUGCACCGUCUAGGUUUGGGAGUAAUUUUAUGGCGGUAACCCCGUCCCCACGGGAAAGGGUGGUGUGCUUUUUUCUGCGUGCGUCUUCACGGGCGUCGCGCGGGCCCCGCUCUUUUUUAUUACGUUUCCUUCGGGGGGCGUGACUCGUGGGUACCCAACCGUGCUGUAAACUGAACCAACGGGAUUGCCUCGUGCAGUUCCGGAGUCUUGUUUCGAGACAUCUGCCAGAUGGGGAGUUUGGCUGGGGCGGCAUAUCUGUUACACGACAACGCAGGUGUCCUAAGGCGAGCUCAGUGGGAACAGAAAUCUCACGUAGAACACAAGCGUAAAAGCUUGCUUGAUUAACGAUUUCCAGUACGAAUCGAGACUGCGAAAGCAAGGCCAGCGAUCCUUUGCGAAGAAUAGGAAAUAUGAACAAAUCAUACCAGAGGUGUCAGAAUAAUUACCACAGGGAUAACUGGCUUGUGGCGGCCAAGCGUUCAUAGCGACGUCGCUUUUUGAUCCUUCGAUGUCGGCUCUUCCUAACCUAGCGCCGCAGAAGACGCUAAGGGUUGGAUUGUUCACCCACUGACAGGGAACGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUUGGUUUUACCCUACUUAGCUGGAAAUUGCGAGAAAAAGAUUAUCCGUGCAAAGCGGACGUCGGGUCGUUCUUGGGCCUGGCGAGCGGUGGGUAGUACUUGGUACGCUCAUCACC |
| 26S gamma ribosomal RNA | 3 | 213 | NA | UAGUGGUAAUGCGAAACACUUGCCAGGUAACAAAUCAAUCCUCCCACGGUGAGCUUUCUUUUCACCAUAAUCCACAUCUCCGGCUUUGCUGGGGCUUGGGCCUUUUUACUUCUCGCGUUGUUCGGAGCGGGGGCUCAAGAUUGAAAAAUGCAGCUCUCCCUACGUACUGUCAUUGUUGUGAGUUCUGCGCAUUAAAGCAAAAACCUGGGGUGU |
| 26S delta ribosomal RNA | 4 | 183 | NA | GUGAGAUUGUGAAGGGAUCUCGCAGGUAUCGUGAGGGAAGUAUGGGGUAGUACGAGAGGAACUCCCAUGCCGUGCCUCUAGUUUCUGGGGUUUGUCGAACGGCAAGUGCCCCGAAGCCAUCGCACGGUGGUUCUCGGCUGAACGCCUCUAAGCCAGAAGCCAAUCCCAAGACCAGAUGCCCAC |
| 26S epsilon ribosomal RNA | 5 | 133 | NA | UACGUCCCUCUCCAAACGAGAGAACAUGCAUGGGCUGGCAUGAGCGGCAUGCUUCACUUCGGUGGGGCUCGAGGGGCAUUUACGUCCCGAGGCGCUGAACCUUGAGGCCUGAAAUUUCAUGCUCAGGGACACA |
| 26S zeta ribosomal RNA | 6 | 76 | NA | UCAUCGAAUCGCCACCUACAAGACUGGAGCUUGCUCCCUCGAAGGCGCCAAGUAUAUUCAUGAUCACAAGACAUUC |
| 5.8S ribosomal RNA | 7 | 171 | NA | AACGUGUCGCGAUGGAUGACUUGGCUUCCUAUUUCGUUGAAGAACGCAGUAAAGUGCGAUAAGUGGUAUCAAUUGCAGAAUCAUUCAAUUACCGAAUCUUUGAACGCAAACGGCGCAUGGGAGAAGCUCUAUUGUGUCAUCCCCGUGCAUGCCAUAUUCUCAGUGUCGAAC |
| 5S ribosomal RNA | 8 | 121 | NA | UCGAGUACGACCAUACUUGAGUGAAAACACCAUAUCCCGUCCGAUUUGUGAAGUUAAGCACUCACAGGCUCAGUUAGUACUGAGGUCAGUGAUGACUCGGGAACCCUGAGUGCCGUACUCC |
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| ribosomal protein L29e | B | 70 | Leishmania Donovani | MAKSKNHTNHNQSSKNHRNGIKGPMPLHLHNSKRGSWLPALVNARRVRKHNQKAALKKRRERIAAFAAKN |
| ribosomal protein L30 | C | 252 | Leishmania Donovani | MTTHSVYGNASDMPAVPAPESAIKRAAFKQQQTENFKKAVVARKAAKAALKKTAYLRARKYSREYRGAEKKLVTLRRQAASHGNYYLEAKPKVAVVTRIRGIAKVNPKQRKILQLLRLRQIFNTVFVKMNKPMENMLRAVEPYIAYGYPSLATVRAMVYKRGYLKINGQRVKITDNQMIKDKYNNADIVCAEDMVNQIYTCGKHFRTVTHGMWPFKLAPPAGGMRQKRRHFVEGGDYGNRDTLINRFLARMI |
| ribosomal protein L30e | D | 104 | Leishmania Donovani | MAKKTKSKVDTINAKLQLVMKSGKYVLGTQQALTTLRQGRSKLIVISNNCPPIRRAEVEYYCTLSKTPIHHYSGNNLDLGTACGKHFRTCVLSVTNVGDSDIAA |
| ribosomal protein L31e | E | 183 | Leishmania Donovani | MKGKVLGKEKKAAIIDARKKDAESRKNRDDKRWKRVLANMDEEKRKKFHGVGNTAKNSRVRGATRASLRKRTGRKPDAVSMEATIHLSKLLKKKTFSKRAPLAIKRIKAFVGRLMKTKDNRIDASLNTYIWHKGVKGVPGRVRVLIQRKSETTEGNKHKHFYTVISNVPVASFKGLTTKTVEQ |
| ribosomal protein L32e | F | 133 | Leishmania Donovani | MVKPTVSKAIVKKRTKRFTRHRYELFPQLSSSWRKPRGEDSPVRRRYKGQKAMPNKGYGSDRATKYITPSGFRSFPINNVEDLYMLVMQNRKYAGVISHTVGARKRKAIARKAMELDVRLANGNAKLRKIANQ |
| ribosomal protein L33e | G | 144 | Leishmania Donovani | MTTSKVHSQRSKKLHQLSAKTSRVNRNRKAPRLYMKGTLAGYTRGLHGQTKQTALVRVENVNTREDATWYVGKRVCYVYHGKKVKRCVRWSKAPARRSTTRALWGRVTRPHGNAGMMRVKFNGASVPASAIGRRIRVYLYPSQI |
| ribosomal protein L34e | H | 168 | Leishmania Donovani | MSCPRVQYRRRMHYATRGNRMKMVRTPGNKLVMQKRAKRSQGIHTPWVLGHKRLGGTKALRHIDARLASRHEKSVSRAYGGVLSHDQVRDRVVRAFLVEEQRIVKQALKEHSKMKLSHKRTANKKKSKQSKKEAIAKKISTKTVSKKKAPAKKATTTRQPVGSKLVKK |
| ribosomal protein L36e | I | 105 | Leishmania Donovani | MSAPTPRTGIIAGFNKGHVTTRRPRQPSPNDRFAVPHKHLRAVKAIIADLVGLSPLEKRVQEFLRVGKEKRALKYCKKRLGDFTAAKKKRSKMEEALRHTTKKHH |
| ribosomal protein L37e | J | 83 | Leishmania Donovani | MTKGTTSMGQRHGRTHILCRRCGRNSYHVQWERCAACAYPRASRRRYNWSVKAIKRRRTGTGRCRYLKVVNRRIANHFKTPKA |
| ribosomal protein L38e | K | 83 | Leishmania Donovani | MPREIKTLKEFLAICSRKDARCVKVKHNPSATKFKVRCSRYLYTLVVNDKKKADKIERSIHPSVKKIAVTARSHAKTNAGSKQ |
| ribosomal protein L39e | L | 51 | Leishmania Donovani | MGRFKPLAVKKKYAKKMNQNKPVPYWIRLRTGNRIKWNEKRRHWRRTKLNY |
| ribosomal protein L43e | M | 92 | Leishmania Donovani | MAKRTVKMGVMGRYGTRYGANPRKRAKKLEVSQHAKHFCSFCGKFAFRRKAVGIWRCDGCSKTVAGGAYTLSTPNNSTVRSTVRRLRELAKI |
| ribosomal protein L44e | N | 106 | Leishmania Donovani | MVNYPKKKVMHCGDARCNAHKSFKVVQYKAGKARLFARGKRRYDRKQSGYGGQTKPVFHKKAKTTKKIVLKLQCSGCKSIRQVVLKRTKHFELNDKKKTGNKDPTW |
| ribosomal protein L18 | O | 305 | Leishmania Donovani | MPFVKVVKNKAYFKRFQVKYRRRREGKTDYHARRQMVLQDKTKFGSPKYRLVVRITNKDIIAQIVQAKIVGDEVVMAAYAHELPAFGIEHGLTNYAAAYATGLLLARRTLAKLGIADKFQGAKEADGSYSAVRTKKDDEGDDEERFPFKAILDVGLARTTTGARVFGVLKGAVDGGMAVPHRPNRFPGYNKEKSSLDAKVHRDRIFGKHVAEYLKQVKEEASSNPDEKCVQFSRYMAAKVLPESIEGMYKKAHAAIRADPSKSLPKKAKKEGVAHKSYKTKKLSGAEKRAAAKAKVAAIRERLGK |
| ribosomal protein L18e | P | 198 | Leishmania Donovani | MGVDLTGISKKSRVIRHHTYSTNPYIKLLIKLYKFLAKRTSSGFNKVVYQRLIKSRSNRAPISLSRIAVVMKRKAVFTAKSKAAPIAVVVGDVLDDVRMARIPAMRVCALRFSKSARQSIVAAGGECLTFDQLAMIAPTGKNTYLLRGRKSGRESVRHFGASGVPGSHSKPYATNRGKETKRGRRTGRSYKRKAFRHV |
| ribosomal protein L19e | Q | 245 | Leishmania Donovani | MVSLKLQARLASSILGCGRARVWLDPNEAVEIQNANSRKSVRKLIKDGFIIRKPVKVHSRARWRKMKEAKDMGRHNGVGRREGSREARMPSKELWMRRLRILRRLLRKYRADKKIDRHVYRDLYVRAKGNVFRNKRNLVEHIHKIKNEKKKERQLAEQLAAKHLRDEQNRNKARKQELRKREKERERARRDDAAAAAQKKKADAAKKSAASAAKSAAPAAKSAAPAAKVAAPATKGAAPVKKSKK |
| ribosomal protein L20e | R | 179 | Leishmania Donovani | MVKPHLRHYQVVGRESPSEKNPEPTVYKFEVFAPNFVVAKSRFWRMMRVKNKVKATHGDVLSCKVVKDAKLVARNYLVDIAYYSQRCGYTRMVKEFRDVSKTGAVSQAYHDLASRHRARYHNIEVLNVKSIPDHEVKHLSIAQYHAPNLSFPLLQRRIKAARKDRAIFVKKNTKRAVVA |
| ribosomal protein L21e | S | 159 | Leishmania Donovani | MVHSYGYKSGTRHLFAKKFRKHGAPSVSTILTNIKVGDYVDVVADSAVREGMPHKYYHGRTGIVWNVTPRGVGVIINKPVRTRTLRKRICVRFEHVRKSRCQEAFKAKEHQFQAYLAAKKAGKALPPLKKSSRMGGIVRPKNVEVLARRVADYEAMVPY |
| ribosomal protein L22 | T | 166 | Leishmania Donovani | MTHYSRKPQVSSKSAKAKVSDLRCHYKNTFETANVINGMPLRKAQQLYRQVLAKTRCIPFKRYNGKIGRTAQAKEWGQTKGRWPRKSVVAMMSLLKNAEANAIEKGLDPNQMVIKHVQVDQAARMRRRTYRAHGRITPYMCSPCHVQLFMSEKKERVPTPKSAPKK |
| ribosomal protein L22e | U | 129 | Leishmania Donovani | MVAVRAKVGSRSYVRQKQLAKGKKVFKIDCSIPAADGIFSEDVLGNFEQFFQDNTKLNGRKGKLSDKVRLSMNDNVLTISTTMAYRKKYFKYLTKKFLKKKDLRDWIRILATGKGTYQLKYFNIQDQEE |
| ribosomal protein L23 | V | 145 | Leishmania Donovani | MPLAQKTAKKAAPKDAKATKVVKVTKRKSYTRPQFRRPHTYRKPAMAKPSNRVTVESKDIAAFSVIRYPLTTDKAMKKIEENNTLTFIVDSRANKTEIKKAMRKLYQVKAVKVNTLIRPDGLKKAYIRLSAAHDALDTANKIGLV |
| ribosomal protein L24 | W | 143 | Leishmania Donovani | MASIKCGSRRKARRAHFQAPSHVRRVLMSAPLSKELRAKYNVRAMPVRKDDEVIVKRGTFKGREGKVTACYRLKWVILIDKVNREKANGSTVAVGIHPSNVEITKLKLTHHRKSILERKDRSSKSDKGKGKISAADKAMQQMD |
| ribosomal protein L24e | X | 124 | Leishmania Donovani | MRTIECEFSHFAVHPGHGRRYVPFAFLSTKPVLTFSRPKCFALYMRKKNPRFIPWTRTYRRIHRKTTTDRVNRRRAARAVRVQRAIVGADLSYIQEVRAARKEDRSAKAKAIRAEVAERKAAKK |
| ribosomal protein L27e | Y | 134 | Leishmania Donovani | MTKFLKPGKVVIVTAGRYAGHKAVIVQNSDIATKERPYGRALLAGIKKYPKKVVRGMSKQTIARRSQVGVFLRVVNHKHFLPTRYNVDMSKELRGKINVSDASKRSRSKRLVRHVFQARYNAGSSMWFFQRLRF |
| ribosomal protein L28e | Z | 147 | Leishmania Donovani | MSHSVDLQWILVRQNSRFLQKRGGIRMSNDPFNNNGNWTKRHCGFLNEKAAVVKPAKGGAICVTVKDGSSNNKPRQTYRKTVHAAGVRASDVSRAVAAVRPDLADVSFRRARRMACIASRTAKVAAARKARSEKIKFSRKSVRAKRH |
| ribosomal protein L2 | A | 260 | Leishmania Donovani | MGKTVLSCRKGNGSVYQVHGHKRLGPAKLRILDYAERHGYMRGVVKSIEHEAGRGAALARVEFRHPYKFRRVKELMVAPEGMFTGQSVFCGQKAPLAIGNVLPLGQITEGCIVCNVEAKPGDRGTLARASGDYCIIISHNHETGRTRLKLPSGQKKSVPSTSRAMIGIISGGGRIEKPVLKAGNSFYRFRGKRNCWPKVRGVARNPVEHPHGGGNHQHIGHPSTVSRHSPPGQKVGLIAARRTGRIRGGKAVKGAWHPEE |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2016-01-21 Deposition Author(s): Bashan, A. , Halfon, Y. , Jaffe, C.L. , Matzov, D. , Rozenberg, H. , Shalev-Benami, M. , Skiniotis, G. , Yonath, A. , Zackay, A. , Zhang, Y. , Zimmerman, E.