Structure of PDB 8i9r Chain CP Binding Site BS01

Receptor Information

>8i9r Chain CP (length=324) Species: 759272 (Thermochaetoides thermophila DSM 1495)

YTNQLLKDICAYYGYNEYLAEKLLNLFPPREAFAFFEANETPRPVVIRTN
TLRTHRRDLAQALINRGVTLEPVGKWSKVGLQVFDSKVPLGATPEYLAGH
YILQAASSFLPVMALCPQENERCLDMAAAPGGKTTHMAALMKNTGVIFAN
DPSKSRAKGLIGNIHRLGVRNTIVCNYDAREFPRVIGGFDRVLLDAPCSG
TGVICKDPSVKTNRDAKDFMQLPHTQKQLLLAAIDSCNHASKTGGYIVYS
TCSVCVEENEEVVNYALSRRPNVKLVETGLPFGKEGFTSYMGKTFHPSLK
LTRRFYPHLYNVDGFFVAKFKKIG

Ligand information

>8i9r Chain C1 (length=2048)

uugaccucggaucagguaggaggacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaacagggauugcccuaguaacggcgagugaagc
ggcaacagcucaaauuugaaagcuggcuucggcccgcguuguaauuugga
gaggaugcuuugggcgaggcuccuucugaguucccuggaacgggacgcca
cagagggugagagccccguauaguuggaagccaagccuguguaaagcucc
uucgacgagucgaguaguuugggaaugcugcucaaaaugggagguaaauu
ucuucuaaagcuaaauaccggccagagaccgauagcgcacaaguagagug
aucgaaagaugaaaagcacuuugaaaagaggguuaaauagcacgugaaau
uguugaaagggaagcgcuugugaccagacuugcgcccggcggaucauccg
guguucucaccggugcacuccgccgggcucaggccagcaucgguucuggc
ggggggauaaaggcccagggaauguggcuccuccgggaguguuauagccc
uggguguaauacccucgccgggaccgaggaccgcgcucugcaaggaugcu
ggcguaauggucaccagcgacccgucuugaaacacggaccaaggagucaa
gguuuugcgcgaguguuuggguguaaaacccgcacgcguaaaggugagag
cuucggcgcaucaucgaccgauccugauguauucggauggauuugaguag
gagcguuaagccuuggacccgaaagauggugaacuaugcuugagcauggg
ggcgaaagacuaaucgaaccaucuaguagcugguuaccgccgaaguuucc
cucaggauagcagugucgaccuucaguuuuaugagguaaagcuuuaaaua
uguaagaagcccuuguuacuuaacugaacgugggcauucgaauguaucga
cacuagugggccauuuuugguaagcagaacuggcgaugcgggaugaaccg
aacgcgggguuaaggugccggaguggacgcucacaaaaggcguuaguaca
ucuuauguacuagcccugggcgcucaagcgucccacccauaccccgcccu
caggguagaaacgaugcccugaggaguaggcggccguggaggucagugac
gaagccuagggcgugagcccgggucgaacggccucuagugcagaucuugg
ugguaguagcaaauacuucaaugagaaggugaacagccucugugauagaa
caauguagauaagggaagucacugucccuaucuacuaucuagcgaaacca
cagccaagggaacgggcuuggcaaaaucagcggggaagacccuguugagc
uugacucuaguuugacauugugaaaagacauaggagguguagaauaggug
ggagcuucggcgccagugaaauaccacuacuccuauuguuuuuuuacuua
uucaaugugaagacauugucagguggggaguuggcggcacaucugugcag
guguccuaaggggggcucauggagaacagaaaucuccaguagaacaaaag
gguaaaaguccccuugauuuugauuuucagugugaauacaaaccaugaaa
guguggccuccuuuagucccucgaaauuugaggcuagaggagaaaaguua
ccacagggaugaccgucgugagacagguuaguucccuacugauacucguc
gcaaugguaauucagcuuaguacgagaggaaccgcugauucagauaauug
guuuuugcgguuguccgaccgggcagugccgcgaagcuaccaucugcugg
auuccaugccagaacgcgacgauaacccgcacgguagacguauaagaaua
ggcuccggccucguauccuagcaggcgauuccuccgccggccucgaagug
gccgucgguaauucgcguauugcaauuuagacacgcgcgggaucaaaucc
uuugcagacgacuuagaugugcgaaaggguccuguaagcaguagaguagc
cuuguuguuacgaucugcugaggguaagcccuccuucgccuagauuuc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8i9r 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): I447 S550 Y551 G553
• Binding residue (residue number reindexed from 1): I186 S289 Y290 G292

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0008168 methyltransferase activity
• GO:0008173 RNA methyltransferase activity
• GO:0008757 S-adenosylmethionine-dependent methyltransferase activity
• GO:0009383 rRNA (cytosine-C5-)-methyltransferase activity

Biological Process

• GO:0000470 maturation of LSU-rRNA
• GO:0001510 RNA methylation
• GO:0006396 RNA processing
• GO:0032259 methylation
• GO:0042254 ribosome biogenesis
• GO:0070475 rRNA base methylation

Cellular Component

• GO:0005730 nucleolus

External links

• PDB: RCSB:8i9r, PDBe:8i9r, PDBj:8i9r
• PDBsum: 8i9r
• PubMed: 37129998
• UniProt: G0SHQ0