6AZ1
Cryo-em structure of the small subunit of leishmania ribosome bound to paromomycin
PDB DOI: 10.2210/pdb6az1/pdb
Classification: RIBOSOME/ANTIBIOTIC Organism(s): Escherichia Coli , Leishmania Donovani , Synthetic Construct
Deposited: 2017-09-09 Deposition Author(s): Bashan, A. , Jaffe, C.L. , Matzov, D. , Rozenberg, H. , Shalev-Benami, M. , Skiniotis, G. , Yonath, A. , Zhang, Y. , Zimmerman, E.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 2.7 Å
Cryo-em structure of the small subunit of leishmania ribosome bound to paromomycin
Bashan, A. , Jaffe, C.L. , Matzov, D. , Rozenberg, H. , Shalev-Benami, M. , Skiniotis, G. , Yonath, A. , Zhang, Y. , Zimmerman, E.
Primary Citation of Related Structures: 6AZ1
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| ribosomal protein S25e | A | 120 | Escherichia Coli , Leishmania Donovani , Synthetic Construct | MPPKAGQTKKAKMEAANKGAKKTTKKWSKGQSREALQNAVMFDKETYDKLRSEVPKYKLITPSIISDRLKIAVSIAAAGLKQLCREKLIRLVSCSSKTRVYTRIVQAAPAEAAAAAPAAE |
| ribosomal protein S8 | J | 130 | Escherichia Coli , Leishmania Donovani , Synthetic Construct | MTMMSVLANALRTIASAERRGKRQVLIRPSSKVVVKFLQVMQKHGYIGEFEIIDDHRAGKIVVNLNGRLNKCGAICPRFDCATTDYEKWMKNILPSRQFGFVVLTTSLGIMDHEEARSRNTGGKVLGFFY |
| ribosomal protein S8e | K | 220 | Escherichia Coli , Leishmania Donovani , Synthetic Construct | MGIVRSRLHKRKITGGKTKIHRKRMKAELGRLPANTRLGARRVSPVRARGGNFKIRALRLDTGNFAWASEAIAHRVRLLDVVYNATSNELVRTKTLVKNCIVAVDAAPFKRWYAKHYGIDLDADRKTTKAAAAAEKKGRKSVHAAADKYDVNKASPKLQREWIRRRRNHRVEKAIADQLREGRVLARITSRPGQSGRADGILLEGAELQFYLKRLEKKKK |
| ribosomal protein S9 | L | 149 | Escherichia Coli , Leishmania Donovani , Synthetic Construct | MPADKSYALKQVQTFGKKKTAIAVATVTKAAQCNIKVNGVPLQQILPDTLRAKIMEAITVVGSKYYSRLRIDVAVHGGGQVSQAYAARQAIAKGLIAFFQKYHNEVEKAALKDKFLAYDKFLLIADPRRCEPKKWGRHSARTRFTKSYR |
| ribosomal protein S10 | M | 116 | Escherichia Coli , Leishmania Donovani , Synthetic Construct | MDYPKKTQAAPAEGQTVRLTITSRNAKAVESVTSQLLMRARDEKVTIHGPVRLPTRTLKITTRKTPCGNGTNTWDTFELKIYKRIIDLHAPTEQVKKITSFTMESGVDVSITILDR |
| ribosomal protein S10e | N | 153 | Escherichia Coli , Leishmania Donovani , Synthetic Construct | MWCARTRTGSHSHHPTQPGSPIDCAEAAPRRMSTYVPKPSRDNVYRFFFTEGVIACKKDRMGTWTGTLGGNTFTVPCIQVMQLMRSLKSRNLIKEQYAWRHYYWTLNDEGIAYMRSYLHLAPSAMPNTQKPSSVNFEKVTEGRGRGRGRGGRG |
| ribosomal protein S11 | O | 144 | Escherichia Coli , Leishmania Donovani , Synthetic Construct | MSKKQEVKAYGPNVKKGDLVYGVVHIYASFNDTFVHVTDTSGRETYVKVTGGMKVKADRDESSPYAAMMAAQDVVARCKECGINALHVKMRAVGGVRTKSPGPGAQAALRALARAGMKIGRIEDVTPIPTDSTRRKGSRRGRRL |
| ribosomal protein S12 | P | 143 | Escherichia Coli , Leishmania Donovani , Synthetic Construct | MTKTNGQNAARKLVRLRRRNRWADKGWKRAHTFAAKKANPFGGSSHAKGIVLEKIGVGAKQPNSAIRKCVRVQLIKNDKKIIAFVPNDGCLHFIEENDEVLVSGFGRSGHAVGDIPGVRFKIVKVSSVGLYALYRQKKEKPRN |
| ribosomal protein S12e | Q | 141 | Escherichia Coli , Leishmania Donovani , Synthetic Construct | MAEETVRVEVPAVEENVVVDVAPESLEDAVRIVIQKALEANGLVRGLSEVARTLDCKTAHMCILADDCEDEEYKKLVTALAKQGNIDLINVEEREKLAQWAGLVRRDVAGEVTKTLKCSSVAIRDFGERTKALDYLLSQLH |
| ribosomal protein S13 | R | 153 | Escherichia Coli , Leishmania Donovani , Synthetic Construct | MSLTLIPDHFQHIVRLLNTNVEGKRKVPFALRMVKGVGIRFAYLVCKKAGIDVERRAGTLTAEELEKIAEIIADPAKFKIPDWFLNRQRDPKTGKTEHLSSSMVDTRLREDLERLKKIRAHRGVRHAYGLRVRGQHTCTTGRHGKTVGVSRGK |
| ribosomal protein S14 | S | 57 | Escherichia Coli , Leishmania Donovani , Synthetic Construct | MGHLDQWRSRQKIGMGKGARCCVICSNQKALIRKYELNVCRQCFRENAEHIGFTKLR |
| ribosomal protein S26e | B | 112 | Escherichia Coli , Leishmania Donovani , Synthetic Construct | MTTKRRNHGRSKPAHSRGRVKPIHCFNCGRLTPKDKAVGRFVVRRMLDAASARDVAEASPVYGANFPMPKLYMKQRFCIACAIHSRTVRARPVGNRKIRYTRKVPFRPAGKK |
| ribosomal protein S15 | T | 151 | Escherichia Coli , Leishmania Donovani , Synthetic Construct | MVRMHGNGRGKASSALPYRRTPPAWLKIASRNVVKMVCKSSRKGMMPSQIGMELRDSMGIAQVKNVTGRKILRILKHSGLAPEIPEDLYFLVKRATQMRKHLERHTTDRDTKYRLILVESRIHRLARYYKRVKQLPPTWKYESSTASAMVA |
| ribosomal protein S17 | U | 173 | Escherichia Coli , Leishmania Donovani , Synthetic Construct | MSAAPQYYHAHQVDATIQHQKAYQRQTAVNENMHRSSRKHVNKSGHIRYAKKIGLGFKTPAKALNGKYIDRKCPFTSNVVIRGRILRGIVHSTKMHRTIVIRRNYLHFIKKYQRYQKRHKSLAVHCSPAFDPKQGDEVVVGQCRPLSKTIRYNVLEVVSKSAADKMGKKFAKN |
| ribosomal protein S17e | V | 143 | Escherichia Coli , Leishmania Donovani , Synthetic Construct | MGKIRTKTVKRASRQVVEKYYSKLNFDFYQNKRVIMDVTIAESKKLKNKIAGYTTHIMKRLARGPVRGISLKLQEEERERRMDHAPATSDVDKAIQSGVSVDKRTMQMLQRLEIGVPRRVKRADAAVAKVKAAPRRRQQKSSK |
| ribosomal protein S19 | W | 152 | Escherichia Coli , Leishmania Donovani , Synthetic Construct | MASNITAERYEQLKKERTFHKFTYRGLEIDPLLALSEEEFRALVHARARRNMNRHVDRRPPVLLKRLREAKKHVKVGEKPKAVKTHLRDVVITPEMVGSVVAIYNGHQFNAVEIKGEMIGHYLGEFSMSYRPVLHGRPGVGATHSSRFIPIK |
| ribosomal protein S19e | X | 179 | Escherichia Coli , Leishmania Donovani , Synthetic Construct | MYSPARMSFIRRVTNPSCIMAALKNKIHRIGKRKGASLKDVSAWRWIKTAARHFKQEGKIFVPNCTEIMKSSHGRERAPQNPDWYYIRCAAVLRAIYLRPGVGYGGLSKRFGNKKNYGSRPEHTVTSSTGPLHWACKSLTKLGLVEPGAQSGQRLTRKGHKFADSLAFQVQIRKFGASK |
| ribosomal protein S21e | Y | 159 | Escherichia Coli , Leishmania Donovani , Synthetic Construct | MATIGMFNEEGENVDLYIPRKCHATNTLIEAHDHAAVQISIANVGPNGVINGTTTTLCIAGYLRSQGESDHAINHITIDRGIMRIKTGKPKRVSKSKSKKPTAGAAGQKGARPPAQKGARPSGQKGARPPAQKGARPPAQKGARPPAQKGAAPARKNRA |
| ribosomal protein S24e | Z | 137 | Escherichia Coli , Leishmania Donovani , Synthetic Construct | MVFQKKKAEVCIRTSQFKVNKLLNRKQFIVEVNHPHWCGTVPTQLIRKKLATLYKVPDASQVSLFGFKTKFGGGKTTGFGLIYDDLASLKRFEPNYRKTRMGFGKARLPARKSVKERRNRNKKLRGKAKGKQVAKKK |
| ribosomal protein S3 | C | 219 | Escherichia Coli , Leishmania Donovani , Synthetic Construct | MGPLSKKRMIIRDGVFYAELFEFLKRELAEEGFSGVSYHVTTLRTEIVIKATKTREVLGVNGRRIRELTACIQQRFNYKEGKLQLYVERVEVRGLSAMAQVESLRFKLLSNLQVRRAAMGIIRYVMESGAKGCEVTVGGKIKGQRAKSMTFRDGYMIKSGTAHKSFVDSACRHCYMRAGCIGVKVKIMLPGDSTGRNGPSEPLPDVITVIEPKQITASE |
| ribosomal protein S4 | D | 190 | Escherichia Coli , Leishmania Donovani , Synthetic Construct | MRNYNNFNRVWKAPRRPFEKERLDREMKLCGQYGLRCKREIWRVNMTLSKMRRTARLLLTLPENHPRRLLEGSAIMRRCHEYGFLDEEKDKLDYVLSLTVPDILERRLQTIVFKAGLAKSVHHARVLIQQRHIAVAKQIVTIPSFIVRVSSERHIAFADASPFGNGRPGRVKRVRAKAAKRHAGGGDDDE |
| ribosomal protein S4e | E | 273 | Escherichia Coli , Leishmania Donovani , Synthetic Construct | MAKKHLKRLYAPKDWMLSKLTGVFAPRPRPGPHKLRECLPLLVIIRNRLKYALNAREGEMILRQGLVHVDNHPRRDGKYPAGFMDVVEIPKTGDRFRLMYDVKGRFALVSLSEAEAQIKLMKVVNLYTATGRVPVAVTHDGHRIRYPDPHTSIGDTIVYNVKEKKCVDLIKNRQGKAVIVTGGANRGRIGEIVKVECHPGAFNIAHLKDASGAEFATRAANIFVIGKDLNHLQVTVPKQQGLRMNVIQEREERLIAAEARKNAPARGARKARK |
| ribosomal protein S5 | F | 265 | Escherichia Coli , Leishmania Donovani , Synthetic Construct | MADTQPAQEAPAADVPRAERNFGRGRGGRGGRGRGRGGPGEEKEWVPCTKLGRLVKAQKVTSLEEIFLFSMPIKEHQIVDTLIAEGQLHDEMMKIYPVQKATSAGQRTRFKAFNVVGDCDGHIGIGARVGKEVSLAIRASMIAAKLNIVPVRRGYWGNKIGEPHTIPMKVTGKCGSVAVRLVPAPRGTGIVAAPVPKKILEFAGVEDVYTSSRGKTRTHGNLIMATFYALRKTYGFLTPDLWAETEPSRDPTDEHAELLAEMTTA |
| ribosomal protein S6e | G | 249 | Escherichia Coli , Leishmania Donovani , Synthetic Construct | MKLNIAYPRNGTVKQFEISDEVLRRVQLQDYRLGNEVDGAIFGSEFKGYIFRLRGGSDKDGFPMVPGVLASSRVSLLVKRGAIGFNTFRGYQGERRRKNVRGCVLASDIALVNVTISKVGDQPIEGVTDTTAPRRLGPKRASKIRKLFNLSRTEDVRKYVVRRRVVKSGKKDRLKAPKIQRLITPRVKARRAKKAKDAIAKVRASAAERREYLRLIASNRRALRQRDHSKKHTQKVHAQRAEVAAFQKK |
| ribosomal protein S7 | H | 190 | Escherichia Coli , Leishmania Donovani , Synthetic Construct | MSSKTPKLFNKWSFEGLETSELALRDHISTTAAYVPHTSGRWQKRRFHKARMPIVERLANGLMFKGRGNGRKLQAARLLKHTLEIIHLLTDENPLQVVVDAVSKGAPREDSTRVGSGGVVRRQAVDVSPMRRVNEAIYQMCKGAREAAFRNLKSMPECLADEIVNASKGSSNSYAIKKKDEVERVAKANR |
| ribosomal protein S7e | I | 200 | Escherichia Coli , Leishmania Donovani , Synthetic Construct | MQPYLRKLRKLKRGKPSDLEESVAKALFELETSHKTLRQELPRFHVNTVREVKVPRSKKTVLVVFYPLRFLMLVRKVQRALTSELEKRHPGYLVMLVAQRKITKRPTDVYKLQKVQRSKTSTAVFENILNDMIYPSDVVGRRWRCRTDGSKLMKVFLDARDRKRVESRLRAVAYVYKQLTHRRVSFGFMWNPKLQQVSTR |
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| ribosomal RNA 18S | 1 | 2203 | NA | GAUCUGGUUGAUUCUGCCAGUAGUCAUAUGCUUGUUUCAAGGACUUAGCCAUGCAUGCCUCAGAAUCACUGCAUUUGCAGGAAUCUGCGCAUGGCUCAUUACAUCAGACGUAAUCUGCCGCAAAAAUCUUGCGGUUUCCGCAAAAUUGGAUAACUUGGCGAAACGCCAAGCUAAUACAUGAACCAACCGGGUGUUCUCCACUCCAGACGGUGGGCAACCAUCGUCGUGAGACGCCCAGCGAAUGAAUGACAGUAAAACCAAUGCCUUCACUGGCAGUAACACCCAGCAGUGUUGACUCAAUUCAUUCCGUGCGAAAGCCGGCUUGUUCCGGCGUCUUUUGACGAACAACUGCCCUAUCAGCUGGUGAUGGCCGUGUAGUGGACUGCCAUGGCGUUGACGGGAGCGGGGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUAGCUACCACUUCUACGGAGGGCAGCAGGCGCGCAAAUUGCCCAAUGUCAAAACAAAACGAUGAGGCAGCGAAAAGAAAUAGAGUUGUCAGUCCAUUUGGAUUGUCAUUUCAAUGGGGGAUAUUUAAACCCAUCCAAUAUCGAGUAACAAUUGGAGGACAAGUCUGGUGCCAGCACCCGCGGUAAUUCCAGCUCCAAAAGCGUAUAUUAAUGCUGUUGCUGUUAAAGGGUUCGUAGUUGAACUGUGGGCUGUGCAGGUUUGUUCCUGGUCGUCCCGUCCAUGUCGGAUUUGGUGACCCAGGCCCUUGCAGCCCGUGAACAUUCAAAGAAACAAGAAACACGGGAGUGGUUCCUUUCCUGAUUUACGCAUGUCAUGCAUGCCAGGGGGCGUCCGUGAUUUUUUACUGUGACUAAAGAAGCGUGACUAAAGCAGUCAUUUGACUUGAAUUAGAAAGCAUGGGAUAACAAAGGAGCAGCCUCUAGGCUACCGUUUCGGCUUUUGUUGGUUUUAAAGGUCUAUUGGAGAUUAUGGAGCUGUGCGACAAGUGCUUUCCCAUCGCAACCUCGGUUCGGUGUGUGGCGCCUUUGAGGGGUUUAGUGCGUCCGGUACGAGCUCCGGUUCGUCCGGCCGUAACGCCUUUUCAACUCACGGCCUCUAGGAAUGAAGGAGGGUAGUUCGGGGGAGAACGUACUGGGGCGUCAGAGGUGAAAUUCUUAGACCGCACCAAGACGAACUACAGCGAAGGCAUUCUUCAAGGAUACCUUCCUCAAUCAAGAACCAAAGUGUGGAGAUCGAAGAUGAUUAGAGACCAUUGUAGUCCACACUGCAAACGAUGACACCCAUGAAUUGGGGAUCUUAUGGGCCGGCCUGCGGCAGGGUUUACCCUGUGUCAGCACCGCGCCCGCUUUUACCACCUUACGUAUCUUUUCUAUUCGGCCUUUACCGGCCACCCACGGGAAUAUCCUCAGCACGUUUUCUGUUUUUUCACGCGAAAGCUUUGAGGUUACAGUCUCAGGGGGGAGUACGUUCGCAAGAGUGAAACUUAAAGAAAUUGACGGAAUGGCACCACAAGACGUGGAGCGUGCGGUUUAAUUXGACXCAACACGGGGAACUUUACCAGAUCCGGACAGGAUGAGGAUUGACAGAUUGAGUGUUCUUUCUCGAUUCCCUGAAUGGUGGUGCAUGGCCGCUUUUGGUCGGUGGAGUGAUUUGUUUGGUUGAUUCCGUCAACGGACGAGAUCCAAGCUGCCCAGUAGAAUUCAGAAUUGCCCAUAGGAUAGCAAACUCAUCGGCGGGUUUUACCCAACGGUGGGCCGCAUUCGGUCGAAUUCUUCUCUGCGGGAUUCCUUUGUAAUUGCACAAGGUGAAAUUUUGGGCAACAGCAGGUCUGUGAUGCUCCUCAAUGUUCUGGGCGACACGCGCACUACAAUGUCAGUGAGAACAAGAAAAACGACUUUUGUCGAACCUACUUGAUCAAAAGAGUGGGGAAACCCCGGAAUCACAUAGACUCACUUGGGACCGAGGAUUGCAAUUAUUGGUCGCGCAACGAGGAAUGUCUCGUAGGCGCAGCUCAUCAAACUGUGCCGAUUACGUCCCUGCCAUUUGUACACACCGCCCGUCGUUGUUUCCGAUGAUGGUGCAAUACAGGUGAUCGGACAGGCGGUGUUUUAUCCGCCCGAAAGUUCACCGAUAUUUCUUCAAUAGAGGAAGCAAAAGUCGUAACAAGGUAGCUGUAGGUGAACCUGCAGCUGGAUCAUUU |
| tRNA-Phe | 2 | 76 | NA | GCGCGGAUAGCUCAGUCGGUAGAGCAGGGGAUUGAAAAUCCCCGUGUCCUUGGUUCGAUUCCGAGUCCGCGCACCA |
| P-site tRNA | 3 | 77 | NA | CGCGGGGUGGAGCAGCCUGGUAGCUCGUCGGGCUCAUAACCCGAAGAUCGUCGGUUCAAAUCCGGCCCCCGCAACCA |
| E-site tRNA | 4 | 76 | NA | GCGCGGAUAGCUCAGUCGGUAGAGCAGGGGAUUGAAAAUCCCCGUGUCCUUGGUUCGAUUCCGAGUCCGCGCACCA |
| mRNA | 5 | 13 | NA | CACCAUGUUCAAA |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2017-09-09 Deposition Author(s): Bashan, A. , Jaffe, C.L. , Matzov, D. , Rozenberg, H. , Shalev-Benami, M. , Skiniotis, G. , Yonath, A. , Zhang, Y. , Zimmerman, E.