Structure of PDB 4u50 Chain s9 Binding Site BS01

Receptor Information

>4u50 Chain s9 (length=185) Species: 559292 (Saccharomyces cerevisiae S288C)

PRAPRTYSKTYSTPKRPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSK
IRRAARDLLTRDEKDPKRLFEGNALIRRLVRVGVLSEDKKKLDYVLALKV
EDFLERRLQTQVYKLGLAKSVHHARVLITQRHIAVGKQIVNIPSFMVRLD
SEKHIDFAPTSPFGGARPGRVARRNAARKAEASGE

Ligand information

>4u50 Chain 6 (length=1795)

uaucugguugauccugccaguagucauaugcuugucucaaagauuaagcc
augcaugucuaaguauaagcaauuuauacagugaaacugcgaauggcuca
uuaaaucaguuaucguuuauuugauaguuccucuacaugguauaacugug
guaauucuagagcuaauacaugcuuaaaaucucgacccuuuggaagagau
guauuuauuagauaaaaaaucaaugucuucggacucuuugaugauucaua
auaacuuuucgaaucgcauggccuugugcuggcgaugguucauucaaauu
ucugcccuaucaacuuucgaugguaggauaguggccuaccaugguuucaa
cggguaacggggaauaaggguucgauuccggagagggagccugagaaacg
gcuaccacauccaaggaaggcagcaggcgcgcaaauuacccaauccuaau
ucagggagguagugacaauaaauaacgauacagggcccauucgggucuug
uaauuggaaugaguacaauguaaauaccuuaacgaggaacaauuggaggg
caagucuggugccagcagccgcgguaauuccagcuccaauagcguauauu
aaaguuguugcaguuaaaaagcucguaguugaacuuugggcccgguuggc
cgguccgauuuuuucguacuggauuuccaacggggccuuuccuucuggcu
aaccuugaguccuuguggcucuuggcgaaccaggacuuuuacuuugaaaa
aauuagaguguucaaagcaggcguauugcucgaauauauuagcauggaau
aauagaauaggacguuugguucuauuuuguugguuucuaggaccaucgua
augauuaauagggacggucgggggcaucaguauucaauugucagagguga
aauucuuggauuuauugaagacuaacuacugcgaaagcauuugccaagga
cguuuucauuaaucaagaacgaaaguuaggggaucgaagaugaucagaua
ccgucguagucuuaaccauaaacuaugccgacuagggaucgggugguguu
uuuuuaaugacccacucggcaccuuacgagaaaucaaagucuuuggguuc
uggggggaguauggucgcaaggcugaaacuuaaaggaauugacggaaggg
caccaccaggaguggagccugcggcuuaauuugacucaacacggggaaac
ucaccagguccagacacaauaaggauugacagauugagagcucuuucuug
auuuugugggugguggugcauggccguucuuaguugguggagugauuugu
cugcuuaauugcgauaacgaacgagaccuuaaccuacuaaauaguggugc
uagcauuugcugguuauccacuucuuagagggacuaucgguuucaagccg
auggaaguuugaggcaauaacaggucugugaugcccuuagacguucuggg
ccgcacgcgcgcuacacugacggagccagcgagucuaaccuuggccgaga
ggucuugguaaucuugugaaacuccgucgugcuggggauagagcauugua
auuauugcucuucaacgaggaauuccuaguaagcgcaagucaucagcuug
cguugauuacgucccugcccuuuguacacaccgcccgucgcuaguaccga
uugaauggcuuagugaggccucaggaucugcuuagagaagggggcaacuc
caucucagagcggagaauuuggacaaacuuggucauuuagaggaacuaaa
agucguaacaagguuuccguaggugaaccugcggaaggaucauua

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4u50 ?
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): P2 R3 A4 P5 R6 T7 Y8 S9 K10 T11 T14 K16 R17 P18 Y19 K37 N38 K39 K40 R44 S50 R54 K65 F71 E72 R78 R79 R82 K92 S121 H124 R126 V127 T130 Q131 R132 H133 Q139 N142 I143 F146 R149 S152 P163 P169 G170 R171 V172 A173 N176
• Binding residue (residue number reindexed from 1): P1 R2 A3 P4 R5 T6 Y7 S8 K9 T10 T13 K15 R16 P17 Y18 K36 N37 K38 K39 R43 S49 R53 K64 F70 E71 R77 R78 R81 K91 S120 H123 R125 V126 T129 Q130 R131 H132 Q138 N141 I142 F145 R148 S151 P162 P168 G169 R170 V171 A172 N175

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:4u50, PDBe:4u50, PDBj:4u50
• PDBsum: 4u50
• PubMed: 25209664
• UniProt: O13516|RS9A_YEAST Small ribosomal subunit protein uS4A (Gene Name=RPS9A)