Structure of PDB 8cbj Chain P Binding Site BS01

Receptor Information

>8cbj Chain P (length=127) Species: 580240 (Saccharomyces cerevisiae W303)

SYRGVDLEKLLEMSTEDFVKLAPARVRRRFARGMTSKPAGFMKKLRAAKL
AAPENEKPAPVRTHMRNMIIVPEMIGSVVGIYNGKAFNQVEIRPEMLGHY
LGEFSITYTPVRHGRAGATTSRFIPLK

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): P38 A39 R40 R43 R44 R47 F56 K59 R77 H79 R81 N82 Y97 G99 K100 Y115 G117 E118 T122 Y123 T124 V126 H128 R137
• Binding residue (residue number reindexed from 1): P23 A24 R25 R28 R29 R32 F41 K44 R62 H64 R66 N67 Y82 G84 K85 Y100 G102 E103 T107 Y108 T109 V111 H113 R122

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0000028 ribosomal small subunit assembly
• GO:0000054 ribosomal subunit export from nucleus
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042254 ribosome biogenesis

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015935 small ribosomal subunit
• GO:0022627 cytosolic small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8cbj, PDBe:8cbj, PDBj:8cbj
• PDBsum: 8cbj
• PubMed: 37169754
• UniProt: Q01855|RS15_YEAST Small ribosomal subunit protein uS19 (Gene Name=RPS15)