Structure of PDB 8i9x Chain LN Binding Site BS01

Receptor Information

>8i9x Chain LN (length=183) Species: 759272 (Thermochaetoides thermophila DSM 1495)

GALKYLEELSKKKQSDVVRFLLRVRCWEYRQLNVIHRASRPSRPDKARRL
GYKAKQGYVIYRVRVRRGGRQLKYQRSLRATAEERVGRRCSNLRVLNSYW
VNQDSTYKYYEVILVDPNHKAIRRDPRINWICNPVHKHRECRGLTSTGKK
SRGLNKGHRFNKTRAGRRKTWKRHNTLSLWRYR

Ligand information

>8i9x Chain C1 (length=2658)

uugaccucggaucagguaggaggacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaacagggauugcccuaguaacggcgagugaagc
ggcaacagcucaaauuugaaagcuggcuucggcccgcguuguaauuugga
gaggaugcuuugggcgaggcuccuucugaguucccuggaacgggacgcca
cagagggugagagccccguauaguuggaagccaagccuguguaaagcucc
uucgacgagucgaguaguuugggaaugcugcucaaaaugggagguaaauu
ucuucuaaagcuaaauaccggccagagaccgauagcgcacaaguagagug
aucgaaagaugaaaagcacuuugaaaagaggguuaaauagcacgugaaau
uguugaaagggaagcgcuugugaccagacuugcgcccggcggaucauccg
guguucucaccggugcacuccgccgggcucaggccagcaucgguucuggc
ggggggauaaaggcccagggaauguggcuccuccgggaguguuauagccc
uggguguaauacccucgccgggaccgaggaccgcgcucugcaaggaugcu
ggcguaauggucaccagcgacccgucuugaaacacggaccaaggagucaa
gguuuugcgcgaguguuuggguguaaaacccgcacgcguaaggugagagc
uucggcgcaucaucgaccgauccugauguauucggauggauuugaguagg
agcguuaagccuuggacccgaaagauggugaacuaugcuuggauagggug
aagccagaggaaacucugguggaggcucgcugacgugcaagaucgucaaa
ucugagcaugggggcgaaagacuaaccaucuaguagcugguuaccgccga
aguuucccucaggauagcagugucgaccuucaguuuuaugagguaaagcg
aaugaacuuuaaauauguaagaagcccuuguuacuuaacugaacgugggc
auucgaauguaucgacacuagugggccauuuuugguaagcagaacuggcg
augcgggaugaaccgaacgcgggguuaaggugccggaguggacgcucauc
agacaccacaaaaggcguuaguacaucuugacagcaggacgguggccaug
gaagucggaauccgcuaaggacuguguaacaacucaccugccgaauguac
uagcccugaaaauggauggcgcucaagcgucccacccauaccccgcccuc
aggguagaaacgaugcccugaggaguaggcggccguggaggucagugacg
aagccuagggcgugagcccgggucgaacggccucuagugcagaucuuggu
gguaguagcaaauacuucaaugagaacuugaaggaccgaaguggggaaag
guuccaugugaacagcgguuggacauggguuagucgauccuaagccauag
ggaaguuccguuucaaaggggcacucgugccccguguggcgaaagggaag
ccgguuaauauuccggcaccuggauguggguuuugcgcggcaacgcaacu
gaacgcggagacgacggcgggggccccgggcagaguucucuuuucuucuu
aacggucuaucacccuggaaacaguuugucuggagauaggguuuaauggc
cggaagagcccgacacuucugucggguccggugcgcucucgacgucccuu
gaaaauccgcgggagggaauaauucucacgccaggucguacucauaaccg
cagcagguccccaaggugaacagccucugguugauagaacaauguagaua
agggaagucggcuccguaacuugguacggacaggggaaucugcgagauuc
ccacugucccuaucuacuaucuagcgaaaccacagccaagggaacgggcu
uggcaaaaucagcggggaaagaagacccuguugagcuugacucuaguuug
acauugugaaaagacauaggagguguagaauaggugggagcuucggcgcc
agugaaauaccacuacuccuauuguuuuuuuacuuauucaaugugaagac
auugucagguggggaguuccuuuagucccucgaaauuugaggcuagagga
gaaaaguuaccacagggauaacuggcuuguggcggccaagcguagcgacg
ucgcuuuuuggaugcggcucuuccuaucauaccgaagcagaauucgguaa
gcguuggauuguucacccacuaauagggaacgugagcuggaccgucguga
gacagguuagucccuacugaugaacucgucgcaaugguaauucagcuuag
uacgagaggaaccgcugauucagauaauugguuuuugcgguuguccgacc
gggcagugccgcgaagcuaccaucugcuggauaauggcugaacgccucua
agucagaauccaugccagaacgcgacgauacuacccgcacguuguagacg
uauaagaauaggcuccggccucguauccuagcaggcgauuccuccgccgg
ccucgaaguggccgucgguaauucgcguauugcaauuuagacacgcgcgg
gaucaaauccuuugcagacgacuuagaugugcgaaaggguccuguaagca
guagaguagccuuguuguuacgaucugcugaggguaagcccuccuucgcc
uagauuuc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8i9x Mechanism of 5S RNP recruitment and helicase-surveilled rRNA maturation during pre-60S biogenesis.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): G2 L4 K5 E8 K12 K14 Q15 N34 V35 S40 R41 R44 K47 R49 R50 L51 K54 A55 K56 Q57 R67 R68 G69 R71 K93 Y94 Q95 R96 S97 R105 R108 N112 Q123 Y127 K128 N138 H139 K140 R144 R147 W150 V155 H156 K157 H158 C161 R162 L164 S166 K170 S171 R172 L174 K176 G177 H178 R179 F180 N181 K182 R187 R188 K189 W191 R193 H194 W200 R201 Y202 R203
• Binding residue (residue number reindexed from 1): G1 L3 K4 E7 K11 K13 Q14 N33 V34 S39 R40 R43 K46 R48 R49 L50 K53 A54 K55 Q56 R66 R67 G68 R70 K73 Y74 Q75 R76 S77 R85 R88 N92 Q103 Y107 K108 N118 H119 K120 R124 R127 W130 V135 H136 K137 H138 C141 R142 L144 S146 K150 S151 R152 L154 K156 G157 H158 R159 F160 N161 K162 R167 R168 K169 W171 R173 H174 W180 R181 Y182 R183

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8i9x, PDBe:8i9x, PDBj:8i9x
• PDBsum: 8i9x
• PubMed: 37129998
• UniProt: G0RZ88