Structure of PDB 8i9x Chain LP Binding Site BS01

Receptor Information

>8i9x Chain LP (length=169) Species: 759272 (Thermochaetoides thermophila DSM 1495)

RYAATEIAPTKSARARGSYLRVSFKNTRETAQAINGWKLQRALTFLQNVI
DKKEAVPMRRYAGSTGRTAQGKQWGVSRARWPVKSAQFLIGLLKNAEANA
DAKGLDTGNLIIKHIQVNQAPKQRRRTYRAHGRINPYMSNPCHIELILTE
AESHLSSRQRGVRIRRALT

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): R3 Y4 R18 Y21 S25 F26 N28 R30 Q34 R62 Y63 G65 R69 K74 Q75 R80 R82 W83 P84 K86 N97 A100 N101 H116 Q118 V119 N120 Q121 R127 Y130 R135 N137 P138 Y139 M140 S141 H170 S173 R174 R176 G177 V178 R179 R181
• Binding residue (residue number reindexed from 1): R1 Y2 R16 Y19 S23 F24 N26 R28 Q32 R60 Y61 G63 R67 K72 Q73 R78 R80 W81 P82 K84 N95 A98 N99 H114 Q116 V117 N118 Q119 R125 Y128 R133 N135 P136 Y137 M138 S139 H154 S157 R158 R160 G161 V162 R163 R165

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8i9x, PDBe:8i9x, PDBj:8i9x
• PDBsum: 8i9x
• PubMed: 37129998
• UniProt: G0SGY1