Structure of PDB 8i9r Chain CE Binding Site BS01

Receptor Information

>8i9r Chain CE (length=463) Species: 759272 (Thermochaetoides thermophila DSM 1495)

QEFSELNLSEKTTKAIAEMGFTKMTEIQRRAIPPALAGKDVLGAAKTGSG
KTLAFLIPAVEMLSSLRFKPRNGTGAIVVTPTRELALQIFGVARELMKYH
SQTYGVVIGGANRRAEAEKLGKGVNLLIATPGRLLDHLQNTPFVFKNLKS
LIIDEADRILEIGFEDEMRQIVKILPKEDRQTMLFSATQTTKVEDLARIS
LRPGPLYINVDEEKKYSTVEGLEQGYVVVEADKRFLLLFSFLKKMAKKKI
IVFFSSCNSVKYYSELLQYIDLPVLDLHGKQKQQKRTNTFFEFCNAKSGT
LICTDVAARGLDIPQVDWIVQFDPPDDPRDYIHRVGRTARGNNGKGRSLL
FLQPCELGFLAHLKAAKVPVVEYDFPKNKILNVQSQLEKLISTNYYLNQS
AKEGYRSYIHAYASHSLRSVFDVHKLDLVKVAKSFGFSTPPRVDITLGRR
AYGSQPRQGGRYK

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): L197 N222 R224 K229 K232 N368 R516 Q579 G580 G581 R582 Y583 K584
• Binding residue (residue number reindexed from 1): L87 N112 R114 K119 K122 N258 R406 Q458 G459 G460 R461 Y462 K463

Enzymatic activity

• Enzyme Commision number: 3.6.4.13: RNA helicase.

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003723 RNA binding
• GO:0003724 RNA helicase activity
• GO:0004386 helicase activity
• GO:0005524 ATP binding
• GO:0016787 hydrolase activity
• GO:0016887 ATP hydrolysis activity

Biological Process

• GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0006364 rRNA processing
• GO:0042254 ribosome biogenesis

Cellular Component

• GO:0005730 nucleolus

External links

• PDB: RCSB:8i9r, PDBe:8i9r, PDBj:8i9r
• PDBsum: 8i9r
• PubMed: 37129998
• UniProt: G0RYU9