Structure of PDB 8i9w Chain LQ Binding Site BS01

Receptor Information

>8i9w Chain LQ (length=129) Species: 759272 (Thermochaetoides thermophila DSM 1495)

RKAPKSDNVYLKLLVKLYRFLARRTEAPFNKVVLRRLFMSRINRPPVSLS
RIARNLKNGNEKKTVVVVATVTDDNRLLQVPKMEVAALRFTAKARARIEA
AGGRTLTLDQLALEKPTGANTLLLRGPKN

Ligand information

>8i9w Chain C1 (length=2163)

uugaccucggaucagguaggaggacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaacagggauugcccuaguaacggcgagugaagc
ggcaacagcucaaauuugaaagcuggcuucggcccgcguuguaauuugga
gaggaugcuuugggcgaggcuccuucugaguucccuggaacgggacgcca
cagagggugagagccccguauaguuggaagccaagccuguguaaagcucc
uucgacgagucgaguaguuugggaaugcugcucaaaaugggagguaaauu
ucuucuaaagcuaaauaccggccagagaccgauagcgcacaaguagagug
aucgaaagaugaaaagcacuuugaaaagaggguuaaauagcacgugaaau
uguugaaagggaagcgcuugugaccagacuugcgcccggcggaucauccg
guguucucaccggugcacuccgccgggcucaggccagcaucgguucuggc
ggggggauaaaggcccagggaauguggcuccuccgggaguguuauagccc
uggguguaauacccucgccgggaccgaggaccgcgcucugcaaggaugcu
ggcguaauggucaccagcgacccgucuugaaacacggaccaaggagucaa
gguuuugcgcgaguguuuggguguaaaacccgcacgcguaaggugagagc
uucggcgcaucaucgaccgauccugauguauucggauggauuugaguagg
agcguuaagccuuggacccgaaagauggugaacuauaugggggcgaaaga
cuaaccaucuaguagcugguuaccgccgaaguuucccucaggauagcagu
gucgaccuucaguuuuaugagguaaagcgaaugaacuuuaaauauguaag
aagcccuuguuacuuaacugaacgugggcauucgaauguaucgacacuag
ugggccauuuuugguaagcagaacuggcgaugcgggaugaaccgaacgcg
ggguuaaggugccggaguggacgcucaucagacaccacaaaaggcguuag
uacaucuugacagcaggacgguggccauggaagucggaauccgcuaagga
cuguguaacaacucaccugccgaauguacuagcccugaaaauggauggcg
cucaagcgucccacccauaccccgcccucaggguagaaacgaugcccuga
ggaguaggcggccguggaggucagugacgaagccuagggcgugagcccgg
gucgaacggccucuagugcagaucuuggugguaguagcauagaacaaugu
agauaagggaagucggcuccguaacuugguacggacaggggaaucugcga
gauucccacugucccuaucuacuaucuagcgaaaccacagccaagggaac
gggcuuggcaaaaucagcggggaaagaagacccuguugagcuugacucua
guuugacauugugaaaagacauaggagguguagaauaggugggagcuucg
gcgccagugaaauaccacuacuccuauuguuuuuuuacuuauucaaugug
aagacauugucagguggggaguuccuuuagucccucgaaauuugaggcua
gaggagaaaaguuaccacagggauaacuggcuuguggcggccaagcguag
cgacgucgcuuuuuggaugcggcucuuccuaucauaccgaagcagaauuc
gguaagcguuggauuguucacccacuaauagggaacgugagcuggaccgu
cgugagacagguuagucccuacugaugaacucgucgcaaugguaauucag
cuuaguacgagaggaaccgcugauucagauaauugguuuuugcgguuguc
cgaccgggcagugccgcgaagcuaccaucugcuggauaauggcugaacgc
cucuaagucagaauccaugccagaacgcgacgauacuacccgcacguugu
agacguauaagaauaggcuccggccucguauccuagcaggcgauuccucc
gccggccucgaaguggccgucgguaauucgcguauugcaauuuagacacg
cgcgggaucaaauccuuugcagacgacuuagaugugcgaaaggguccugu
aagcaguagaguagccuuguuguuacgaucugcugaggguaagcccuccu
ucgccuagauuuc

........................<<<<<<.....<<....>>......>
>>>>.>.........<<....>>..<<<<<......<<.....>>.....
>>>>>..<<<..<<.......<<.<<<....>>>.>>.......>>....
<<<<<.<<<<<<<<<..<<<<<<..<<....<<<<......>>>>.((..
....<<<.....))>>>....>>..>>>.>>>..>>>>....>>>>>>>>
.>>........<<<<<<<........>>>>>>>.....<<<<<<......
>>>>>>..>>>..................................<<...
.>>...............<<<<....>>>>....................
..............<<<<.<<<<<<.<...<<.<<<<<<<<<.....<<<
<<<....>>>>>>......>>>>>>>>>.>>.<<<<<<<.<<<<<<<<<<
<<<<<.....<.<<<<<<<<......<<<<<....>>>>>.......>>>
>>>>>....>.>>>>>>>>>>>>>>>........<<...>>.....>>>>
>>>....>>>>>>>.>>>>..<<<<.<....>.>>>><<<<<<....<<<
<<<<<.<<<<..<<<..<<<<<.....>>>>>..>>>....<<<<<..<<
....>>...>>>>>.<<<<<<<<....<....>....>>>.>>>.>>...
.>>>>.>>>>>>>>..<<.<...<<<<<<...<.<<>>>.<<.<....>.
>>.>>>>>>......>.>>...<<<<<....<.<<<....>>>.><<<<<
<<<<<....<<.<<<<<<<.....<<<........>>.>.....>>>>>.
..<<<<.<<<<.<......>>>>>.>>>>.....>>>>..>>>>>>>>.>
>..<<<<.<<<<<.....>>>>>.>>>>....<<<......>>>...<<<
<<<<...<<<.(......<<<<<<.....<<..........<<<.<<<<<
<<<<<.......<<<<<.<<<...<<.........>>...>>>.......
..<<......>>...>>>>>...>>>>>>>>>>>>>...........)..
>>...>>>>>>.>>>...>>>>>>><<<<<<<<<.........>>>>>>>
>>....>>>>>...<<<<<<<<.<<......<<<<.<<<<....>>>>>>
>>...>>>>>>>>>>........>>>>>><<.....<<.<<<<.....<<
<<<<.<<<<<<<<....<<<<<<.<..>.>>>>>>...<<<<<<<<<>>.
>>>>>>>>>>.>>>>>>>>>>>..>>>>>>....>>....<<<<<.....
...>>>>>....<<<<<..<<<........<<<<<<.<<<<<<.<<<<<.
<<<<<<<<..<<<<<<<<<<<<<<<<<..........<<<<<..<<....
>>............>>>>>.>>>>>>>.>>>>>>>>>>...<<<<...>>
>>.....>>>>>>>>..>>>>>.<<<<<<<..<<<<<<...>>>>>>>>>
>>>>....>>>>>.>.>>>>>>.............<<<<<<...<<...>
>...>>>>>>.....((...<<<<<<<<<<..<.<<<<<<<......>>>
>>>>...>.<<<.....))..>>>.....>>>>>....>>>>>.<<<<<<
<....>>>.>>>>....>>>.>>>>>....<<<<<<<..<<<<.<.<<<<
<.................>>>>>.><<<<<...<<<<....<<<<<<<<<
<....>>>>>..>>>>>...>>>>..>>>>>.<<<<...<<<<<......
.....>>>>>...>>>>.>>>>....>>>>>>>.....<<<<<.<<.<<<
......<<.......<<<<..>>>>....>>........<<<<.....<<
<.<<<<<.......>>>>>.>>>....>>>>..............>>>>>
.>>>>>...<<<<<<<.............>>....<<<<<<<<<.<<<..
..<<<<....<<<<<......>>>>>...>>>>...>>>....>>>>..>
>>>>...>>>>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8i9w Mechanism of 5S RNP recruitment and helicase-surveilled rRNA maturation during pre-60S biogenesis.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): R44 S49 K59 F63 R66 P71 F72 V75 S83 R84 N86 P89 S91 S93 R94 R97 N101 T113 T115 D116 D117 N118 R119 L120 R132 T134 A135 K136 G161 A162 N163 R168 K171 N172
• Binding residue (residue number reindexed from 1): R1 S6 K16 F20 R23 P28 F29 V32 S40 R41 N43 P46 S48 S50 R51 R54 N58 T70 T72 D73 D74 N75 R76 L77 R89 T91 A92 K93 G118 A119 N120 R125 K128 N129

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0043232 intracellular non-membrane-bounded organelle
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8i9w, PDBe:8i9w, PDBj:8i9w
• PDBsum: 8i9w
• PubMed: 37129998
• UniProt: G0S9B5