Structure of PDB 5ndv Chain S9 Binding Site BS01

Receptor Information

>5ndv Chain S9 (length=174) Species: 559292 (Saccharomyces cerevisiae S288C)

PRAPRTYSKTYSTPKRPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSK
IRRAARDLLTRDEKDPKRLFEGNALIRRLVRVGVLSEDKKKLDYVLALKV
EDFLERRLQTQVYKLGLAKSVHHARVLITQRHIAVGKQIVNIPSFMVRLD
SEKHIDFAPTSPFGGARPGRVARR

Ligand information

>5ndv Chain 2 (length=1712)

uaucugguugauccugccaguagucauaugcuugucucaaagauuaagcc
augcaugucuaaguauaagcaauuuauacagugaaacugcgaauggcuca
uuaaaucaguuaucguuuauuugauaguuccuuuacuacaugguauaacu
gugguaauucuagagcuaauacaugcuuaaaaucucgacccuuuggaaga
gauguauuuauuagauaaaaaaucaaugucuucggacucuuugaugauuc
auaauaacuuuucgaaucgcauggccuugugcuggcgaugguucauucaa
auuucugcccuaucaacuuucgaugguaggauaguggccuaccaugguuu
caacggguaacggggaauaaggguucgauuccggagagggagccugagaa
acggcuaccacauccaaggaaggcagcaggcgcgcaaauuacccaauccu
aauucagggagguagugacaauaaauaacgauacagguuguaauuggaau
gaguacaauguaaauaccuuaacgaggaacaauuggagggcaagucuggu
gccagcagccgcgguaauuccagcuccaauagcguauauuaaaguuguug
caguuaaaaagcucguaguugaacuuugggcccgguuggccggucggauu
uccaacggggccuuuccuucuggcaccaggacuuuuacuuugaaaaaauu
agaguguucaaagcaggcguauugcucgaauauauuagcauggaauaaua
gaauaggacguuugguucuauuuuguugguuucuaggaccaucguaauga
uuaauagggacggucgggggcaucaguauucaauugucagaggugaaauu
cuuggauuuauugaagacuaacuacugcgaaagcauuugccaaggacguu
uucauuaaucaagaacgaaaguuaggggaucgaagaugaucagauaccgu
cguagucuuaaccauaaacuaugccgacuagggaucgggugguguuuuuu
uaaugacccacucggcaccuuacgagaaaucaaagucuuuggguucuggg
gggaguauggucgcaaggcugaaacuuaaaggaauugacggaagggcacc
accaggaguggagccugcggcuuaauuugacucaacacggggaaacucac
cagguccagacacaauaaggauugacagauugagagcucuuucuugauuu
ugugggugguggugcauggccguucuuaguugguggagugauuugucugc
uuaauugcgauaacgaacgagaccuuaaccuacuaaauaguggugcuagc
auuugcugguuauccacuucuuagagggacuaucgguuucaagccgaugg
aaguuugaggcaauaacaggucugugaugcccuuagacguucugggccgc
acgcgcgcuacacugacggagccagcgagucuaaccuuggccgagagguc
uugguaaucuugugaaacuccgucgugcuggggauagagcauuguaauua
uugcucuucaacgaggaauuccuaguaagcgcaagucaucagcuugcguu
gauuacgucccugcccuuuguacacaccgcccgucgcuaguaccgauuga
auggcuuagugaggccucaggaucuggagcggagaauuuggacaaacuug
gucauuuagaggaacuaaaagucguaacaagguuuccguaggugaaccug
cggaaggaucau

...<<<<<...[[[[>>>>>[[[[.((((((................[[[
.[[[..<<....<<....<............>...>>.>>......{{..
......[[[..{{..{{....[[[..................<.....<<
.<<<.....>>>.>>......>.........<<<<<..<......>..>>
>>>[...((((((......<<<<<<<<<<<....>>>.............
.)))))).....]...<<<<..<<<.....>>>.>>>>....]]]...}}
}}..]]].<<<....<<<....<<<<<<<<.......>>>>>>>>>>>..
....>>>...<<<.<<<<....>>>>....>>>.}}.<<.<<<.......
...>>>.>>.<.<<....>>.>...]]]]]].........<<<....<<<
.....>>>..>>>...............<<<<<.......>>.>>>....
..<<..<...........>..>>.........<<<<<((....<.<<<<.
....<<..))>>.......>>>>>>>>>>..))))))]]]].........
[[[{{.......{{...[[[.{{....<<<<<<.<<<<............
..>>>>.>>>>>>.....<<<<<..>>>>>....<<<<<.<<.......<
<...<.......>..<<<<...>>>>....>>......>>.>>..>>>..
.......[[[..((((((((....>>>>>>>>.)))))))).]]].....
}}....<<<<<<.<<...<<<<..<<..<<<<<<.<...<<<......>>
>......>.>>>>>.>.>>.......<<....>>...>>>>..>.>>>>.
>>>...]]]...}}......<<<<<<<...<...<<<<.........>>>
>...>>>>>>>>..........<<<.<<.<<<..<<<<<<<<.<<<....
....>>>>>>>>>>>..>>>...<<..}}>>...>>.....>>>.]]].<
<<......<<<<....>>>>....>>>..]]]]..<<<<<.<<<<<<<..
<<.<<<<<<..<<<.<<<<........<<........>>..........<
<<<<.<....<<<<<........<<.<<<........>>>.>>......>
>>>>.<.<<.<<<..<<<<<<<<.....<<<.<<<<<....>>>...<<<
......>>>...>>.>>>....<<<<<.<<..<<<<..<<<<<.<<<<<<
....>>>>>>...>>>>>..>>>>.>>....<<<<<<.....>>>>>>..
.....>>>>>.....>>.>>>...>.>>>>>>>>....>.>>>>>.....
.>>>>.>>>.....<<<<<<<......<<.....<<..<<<<....>>>>
..>>....>>.......>>>>>>>...........<<<<<<.........
.>>>>>>..........>>>>>>....<<<<<<<<.......>>>>>>>>
......>>...>>>>>>>>>>.>>....<..<<.<..<<<<.<<....<<
<<<<<<.<<<..<.<<......<<<.....>>>......>>.>..>>>.>
>>>>>>>...>>.>>>>...>.>>...>.....<<<<<<<<<....>>>>
>>>>>.......

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ndv Aminoglycoside interactions and impacts on the eukaryotic ribosome.
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): P2 R3 P5 R6 T7 Y8 S9 K10 T11 Y12 T14 K16 R17 Y19 L24 K37 N38 K39 K40 R44 R57 D58 F71 E72 A75 R78 R79 R82 S121 H124 R126 V127 T130 Q131 R132 V141 N142 I143 R149 P163 P169 R171 V172 A173 R174
• Binding residue (residue number reindexed from 1): P1 R2 P4 R5 T6 Y7 S8 K9 T10 Y11 T13 K15 R16 Y18 L23 K36 N37 K38 K39 R43 R56 D57 F70 E71 A74 R77 R78 R81 S120 H123 R125 V126 T129 Q130 R131 V140 N141 I142 R148 P162 P168 R170 V171 A172 R173

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding

Biological Process

• GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0042254 ribosome biogenesis
• GO:0042274 ribosomal small subunit biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015935 small ribosomal subunit
• GO:0022627 cytosolic small ribosomal subunit
• GO:0030686 90S preribosome
• GO:0032040 small-subunit processome
• GO:0043226 organelle
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5ndv, PDBe:5ndv, PDBj:5ndv
• PDBsum: 5ndv
• PubMed: 29208708
• UniProt: O13516|RS9A_YEAST Small ribosomal subunit protein uS4A (Gene Name=RPS9A)