Structure of PDB 8cbj Chain O Binding Site BS01

Receptor Information

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

SQVFGVARIYASFNDTFVHVTDLSGKETIARVTGGMKVKADRDESSPYAA
MLAAQDVAAKCKEVGITAVHVKIRATGGTRTKTPGPGGQAALRALARSGL
RIGRIEDVTPVPSDSTRKKGGRRGRRL

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): N24 D25 F27 T38 R41 T43 M46 K49 D51 R52 E54 P120 V121 P122 S123 D124 T126 R127 K129 G131 R132 R133 R136
• Binding residue (residue number reindexed from 1): N14 D15 F17 T28 R31 T33 M36 K39 D41 R42 E44 P110 V111 P112 S113 D114 T116 R117 K119 G121 R122 R123 R126

Gene Ontology

Molecular Function

• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0000028 ribosomal small subunit assembly
• GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0042254 ribosome biogenesis

Cellular Component

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

External links

• PDB: RCSB:8cbj, PDBe:8cbj, PDBj:8cbj
• PDBsum: 8cbj
• PubMed: 37169754
• UniProt: P06367|RS14A_YEAST Small ribosomal subunit protein uS11A (Gene Name=RPS14A)