Structure of PDB 5wyk Chain SK Binding Site BS01

Receptor Information

>5wyk Chain SK (length=175) Species: 559292 (Saccharomyces cerevisiae S288C)

YSTPKRPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSKIRRAARDLLT
RDEKDPKRLFEGNALIRRLVRVGVLSEDKKKLDYVLALKVEDFLERRLQT
QVYKLGLAKSVHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHIDFAPT
SPFGGARPGRVARRNAARKAEASGE

Ligand information

>5wyk Chain SA (length=1000)

guugauccugcagucauaugcuugucucaaagccaugcaauggcucauua
aaucaguuaucguuuauuugauaguuccuuuacuacaugguauaacugug
guaauucuagagcuaauacaugcuuaaaaucucgacccuuuggaagagau
guauuuauuagauucauaauaacuuuucgaaucgcauggccuugugcugg
cgaugguucauucaaauuucugcccuaucaacuuucgaugguaggauagu
ggccuaccaugguuucaacggguaacggggaauaaggguucgauuccgga
gagggagccugagaaacggcuaccacauccaaggaagggcaggcgcuuac
ccaauccuaauucagggagguagugacaauaaauaacgauacagggccca
uucgggucuuguaauuggaaugaguacaauguaaauaccuuaacgaggaa
caauuggagucuggucagcagccgcgcagcuccaauagcguauauuaagc
ucguaguugaacuuuaauagggacggucgggggcaucaguauucaauugu
cagaggugaaauucuuggauuuauugaagacuaacuacugcgaaagcauu
ugccaaggacguuuucauuaaucaagaacgaauagggaucgggugguguu
uuuuuaaugacccacucggcaccuuacgagaaaucggaguauggucgcaa
ugacggaagggcaccaccaggaguggagccugcggcacucaacacacgcg
cgcuacacugacggagccagcgagccuuggccgagaggucuugguaaaaa
cuccgucgugcaacgaggaauuccuaguaagcgcaagucaucagcuugcg
uugauuacgucccugcccuuuguacacaccgcccgucgcuaguaccgauu
gaauggcuuagugaggccucaggaucugcgcggagaauuuggacaaacuu
ggucauuuagaggaacuaaaagucguaacaagucauuaaagaaauuuaau

............<<.<<<<<<...<......<<<.<<<.....<<.....
...<<<..<<..<<....<<<..................<<....<<.<<
<.....>>>.>>.....>>.........<<<<<..<<....>>..>>>>>
....<<<<<<......>>>>>>.........<<<<..<<<.....>>>.>
>>>....>>>...>>>>..>>>.<<<....<<<....<<<<<<<<.....
..>>>>>>>>>>>......>>>...<<<.<<<<....>>>>....>>>.>
>.<<.<<<..........>>>.>>.<.<<....>>.>.>>>>>>...<<<
<....<<<.....>>>..>>>>........>.....<<.<<<<..<<<<.
...>>>>..>>>>..>>......<<..<...........>..>>......
...<<<<<<.<<...............>>>>>>>>..>>>>>>>>...<.
<<...<<<.<<..>>....<<<<<<.<<...<<<<..<<<.<<<<<<.<.
..<<<......>>>......>.>>>>>>.>>>.......<<....>>...
>>>>..>.>>>>.>>>...>>>...>>.>....<<<..<<<<<<<<.<<<
........>>>>>>>>>>>..>>>....<....>................
..<<<.<<<<<<<..<<.<<<<<<..<<<.<<<<............>>>>
.>>>.....<<<<<<<........<<..<<<<....>>>>..>>......
>>>>>>>............>>>>>>....<<<<<<<<.......>>>>>>
>>......>>...>>>>>>>>>>..........<<.<..<<<<.<<....
<<<<<<<<.<<<..<.<<......................>>.>..>>>.
>>>>>>>>...>>.>>>>...>.>>.........<<<<<<....>>>>>>

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5wyk Molecular architecture of the 90S small subunit pre-ribosome.
• Resolution: 4.5 Å
• Binding residue (original residue number in PDB): N38 K39 H124 V127 T130 Q131 H133 P169 R171 V172 A173 R175 N176
• Binding residue (residue number reindexed from 1): N27 K28 H113 V116 T119 Q120 H122 P158 R160 V161 A162 R164 N165

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:5wyk, PDBe:5wyk, PDBj:5wyk
• PDBsum: 5wyk
• PubMed: 28244370
• UniProt: O13516|RS9A_YEAST Small ribosomal subunit protein uS4A (Gene Name=RPS9A)