Structure of PDB 8cbj Chain Y Binding Site BS01

Receptor Information

>8cbj Chain Y (length=134) Species: 580240 (Saccharomyces cerevisiae W303)

SDAVTIRTRKVISNPLLARKQFVVDVLHPNRANVSKDELREKLAEVYKAE
KDAVSVFGFRTQFGGGKSVGFGLVYNSVAEAKKFEPTYRLVRYGLAEKVE
KASRQQRKQKKNRDKKIFGTGKRLAKKVARRNAD

Ligand information

>8cbj Chain 2 (length=1767)

aucugguugauccugccaguagucauaugcuugucucaaagauuaagcca
ugcaugucuaaguauaagcaauuuauacagugaaacugcgaauggcucau
uaaaucaguuaucguuuauuugauaguuacaugguauaacugugguaauu
cuagagcuaauacaugcuuaaaaucucgacccuuuggaagagauguauuu
auuagauaaaaaaucaaugucuucggacucuuugaugauucauaauaacu
uuucgaaucgcauggccuugugcuggcgaugguucauucaaauuucugcc
cuaucaacuuucgaugguaggauaguggccuaccaugguuucaacgggua
acggggaauaaggguucgauuccggagagggagccugagaaacggcuacc
acauccaaggaaggcagcaggcgcgcaaauuacccaauccuaauucaggg
agguagugacaauaaauaacgauacagggcccauucgggucuuguaauug
gaaugaguacaauguaaauaccuuaacgaggaacaauuggagggcaaguc
uggugccagcagccgcgguaauuccagcuccaauagcguauauuaaaguu
guugcaguuaaaaagcucguaguugaacuuugggcccgguuggccggucg
gauuuccaacggggccuuuccuucuggcuaaccuugaguccuuguggcuc
uuggcgaaccaggacuuuuacuuugaaaaaauuagaguguucaaagcagg
cguauugcucgaauauauuagcauggaauaauagaauaggacguuugguu
cuauuuuguugguuucuaggaccaucguaaugauuaauagggacggucgg
gggcaucaguauucaauugucagaggugaaauucuuggauuuauugaaga
cuaacuacugcgaaagcauuugccaaggacguuuucauuaaucaagaacg
aaaguuaggggaucgaagaugaucagauaccgucguagucuuaaccauaa
acuaugccgacuagggaucgggugguguuuuuuuaaugacccacucggca
ccuuacgagaaaucaaagucuuuggguucuggggggaguauggucgcaag
gcugaaacuuaaaggaauugacggaagggcaccaccaggaguggagccug
cggcuuaauuugacggggaaacucaccagguccagacacaauaaggauug
acagauugagagcucuuucuugauuuugugggugguggugcauggccguu
cuuaguugguggagugauuugucugcuuaauugcgauaacgaacgagacc
uuaaccuacuaaauaguggugcuagcauuugcugguuauccacuucuuag
agggacuaucgguuucaagccgauggaaguuugaggcaauaacaggucug
ugaugcccuuagacguucugggccgcacgcgcgcuacacugacggagcca
gcgagucuaaccuuggccgagaggucuugguaaucuugugaaacuccguc
gugcuggggauagagcauuguaauuauugcucuucaacgaggaauuccua
guaagcgcaagucaucagcuugcguugauuacgucccugcccuuuguaca
caccgcccgucgcuaguaccgauugaauggcuuagugaggccucaggauc
ugcuuagagaagggggcaacuccaucucagagcggagaauuuggacaaac
uuggucauuuagaggaacuaaaagucguaacaagguuuccguaggugaac
cugcggaaggaucauua

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8cbj Molecular basis for recognition and deubiquitination of 40S ribosomes by Otu2.
• Resolution: 3.8 Å
• Binding residue (original residue number in PDB): R8 T9 R10 K11 V12 K21 A33 N34 K37 K49 G59 F60 T62 Q63 F64 K84 Y89 R93 S104 R105 Q106 R108 K109 Q110 K112 N113 K116 K117 G120 T121 K123 R124 K127 K128 R131 R132
• Binding residue (residue number reindexed from 1): R7 T8 R9 K10 V11 K20 A32 N33 K36 K48 G58 F59 T61 Q62 F63 K83 Y88 R92 S103 R104 Q105 R107 K108 Q109 K111 N112 K115 K116 G119 T120 K122 R123 K126 K127 R130 R131

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005739 mitochondrion
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8cbj, PDBe:8cbj, PDBj:8cbj
• PDBsum: 8cbj
• PubMed: 37169754
• UniProt: P0CX31|RS24A_YEAST Small ribosomal subunit protein eS24A (Gene Name=RPS24A)