Structure of PDB 8pv2 Chain CJ Binding Site BS01

Receptor Information

>8pv2 Chain CJ (length=493) Species: 759272 (Thermochaetoides thermophila DSM 1495)

GKAKKKGKSGAARNYMTRTQAVKKLQLSLPDFRKLCIWKGIYPREPRDRR
KVNKSATASTTFYYTKDIQYLLHEPLLQKFREQKALEKKISRALGRGDVS
NAARLERNANLPEKTGKPRYTLNHIIRERYPTFQDALRDLDDCLSMLFLF
ANLPSTTAVPAKMIARCERLCHEFQHYLIVTHSLRKSFLSIKGIYYQANI
QGEDILWLVPYKFNQRIVGDVDFRIMGTFVEFYMTLLGFVNYRLYTSIGL
KYPPKFDQVKDDQGAELAAFSLEGLDPSQLFANFTFFLSRETPRQPLEFI
LRAFGCKRIGWDAVLGEGAFTTDESDPRITHQIIDRPGRYPGRIYVQPQW
VWDSINDEELKPPELYAPGAQLPPHLSPFVKPTQGQYDPTKPLEEQQTEA
EALEAELEDAQAEATLERQRELEAELDPKVKAKLEAKKALERKKKQEAEE
LERAKGMLSKKKRKLFEQMQYSNAKKNAEDAKLRAKRRRIEKE

Ligand information

>8pv2 Chain C1 (length=3056)

uugaccucggaucagguaggaggacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaacagggauugcccuaguaacggcgagugaagc
ggcaacagcucaaauuugaaagcuggcuucggcccgcguuguaauuugga
gaggaugcuuugggcgaggcuccuucugaguucccuggaacgggacgcca
cagagggugagagccccguauaguuggaagccaagccuguguaaagcucc
uucgacgagucgaguaguuugggaaugcugcucaaaaugggagguaaauu
ucuucuaaagcuaaauaccggccagagaccgauagcgcacaaguagagug
aucgaaagaugaaaagcacuuugaaaagaggguuaaauagcacgugaaau
uguugaaagggaagcgcuugugaccagacuugcgcccggcggaucauccg
guguucucaccggugcacuccgccgggcucaggccagcaucgguucuggc
ggggggauaaaggcccagggaauguggcuccuccgggaguguuauagccc
uggguguaauacccucgccgggaccgaggaccgcgcucugcaaggaugcu
ggcguaauggucaccagcgacccgucuugaaacacggaccaaggagucaa
gguuuugcgcgaguguuuggguguaaaacccgcacgcguaaugaaaguga
acguaggugagagcuucggcgcaucaucgaccgauccugauguauucgga
uggauuugaguaggagcguuaagccuuggacccgaaagauggugaacuau
gcuuggauagggugaagccagaggaaacucugguggaggcucgcagcggu
ucugacgugcaaaucgaucgucaaaucugagcaugggggcgaaagacuaa
ucgaaccaucuaguagcugguuaccgccgaaguuucccucaggauagcag
ugucgaccuucaguuuuaugagguaaagcgaaugaacuuuaaauauguaa
gaagcccuuguuacuuaacugaacgugggcauucgaauguaucgacacua
gugggccauuuuugguaagcagaacuggcgaugcgggaugaaccgaacgc
gggguuaaggugccggaguggacgcucaucagacaccacaaaaggcguua
guacaucuugacagcaggacgguggccauggaagucggaauccgcuaagg
acuguguaacaacucaccugccgaauguacuagcccugaaaauggauggc
gcucaagcgucccacccauaccccgcccucaggguagaaacgaugcccug
aggaguaggcggccguggaggucagugacgaagccuagggcgugagcccg
ggucgaacggccucuagugcagaucuuggugguaguagcaaauacuucaa
ugagaacuugaaggaccgaaguggggaaagguuccaugugaacagcgguu
ggacauggguuagucgauccuaagccauagggaaguuccguuucaaaggg
gcaugccccguguggcgaaagggaagccgguuaauauuccggcaccugga
uguggguuuugcgcggcaacgcaacugaacgcggagacgacggcgggggc
cccgggcagaguucucuuuucuucuuaacggucuaucacccuggaaacag
uuugucuggagauaggguuuaauggccggaagagcccgacacuucugucg
gguccggugcgcucucgacgucccuugaaaauccgcgggagggaauaauu
cucacgccaggucguacucauaaccgcagcagguccccaaggugaacagc
cucugguugauagaacaauguagauaagggaagucggcaaaauagauccg
uaacuucgggaaaaggauuggcucuaaggguugguaacaaccaacuuaga
acugguacggacagggggaaucugacugucuaauuaaaacauagcauugc
gauggccagaaagugguguugacgcaaugugauuucugcccagugcucug
aaugucaaagugaagaaauucaaccaagcgcggguaaacggcgggaguaa
cuaugacucucuguagccaaauggauuaacgagauucccacugucccuau
cuacuaucuagcgaaaccacagccaagggaacgggcuuggcaaaaucagc
ggggaaagaagacccuguugagcuugacucuaguuugacauugugaaaag
auuuuuuuacuuauucaaugaagcggggcuggacuugcguccaacuucug
gaguuaagguccuucgcgggccgacccggguugaagacauugucaggugg
ggaguuuggcuggggcggcacaucugugcagguguccuaaggggggcuca
uggagaacagaaaucuccaguagaacaaaaggguaaaaguccccuugauu
uugauuuucagugugaauacaaaccaugaaaguguggccuaucgauccuu
uagucccucgaaauuugaggcuagaggugccagaaaaguuaccacaggga
uggcuuguggcggccaagcguucauagcgacgucgcuuugauccuucgau
gucggcucuuccuaucauaccgaagcagaauucgguaagcguuggauugu
ucacccacuaauagggaacgugagcuggguuuagaccgucgugagacagg
uuaguuuuacccuacugaugaacucgucgcaaugguaauucagcuuagua
cgagaggaaccgcugauucagauaauugguuuuugcgguuguccgaccgg
gcagugccgcgaagcuaccaucugcuggauaauggcugaacgccucuaag
ucagaauccaugccagaacgcgacgauacuacccgcacguuguagacgua
uaagaauaggcuccggccucguauccuagcaggcgauuccuccgccggcc
ucgaaguggccgucgguaauucgcguauugcaauuuagacacgcgcggga
ucaaauccuuugcagacgacuuagaugugcgaaaggguccuguaagcagu
agaguagccuuguuguuacgaucugcugaggguaagcccuccuucgccua
gauuuc

........................<<<<<<.....<...<..>......>
>>>>.>...[.....<<....>>..<<<<<......<<.>...>>.....
>>>>>..<<<..<<.......<<.<<<....>>>.>>.......>>....
<<<<<.<<<<<<<<<..<<<<<<..<<<...<<<<......>>>>.((..
....<<<.....))>>>.>..>>..>>.>>>>..>>>>....>>>>>>>>
.>>........<<<<<<<........>>>>>>>.....<<<<<..(((((
(>>>>>..>>>....].............................<<...
.>>...............<<<<....>>>>....................
..............<<<<.<<<<<<.<...<<.<<<<<<<<<.....<<<
<<<....>>>>>>......>>>>>>>>>.>>.<<<<<<<.<<<<<<<<<<
<<<<<.......<<<<<<<<......<<<<<....>>>>>.......>>>
>>>>>......>>>>>>>>>>>>>>>........<<...>>.....>>>>
>>>....>>>>>>>.>>>>..<<<<.<....>.>>>><<<<<<...<<<<
<<<<<.<<<<..<<<..<<<<<.....>>>>>..>>>...<<....>>..
.....<<<<<..<<....>>...>>>>>.<<<<<<<<...<<....>>..
.>>>>.>>.>>....>>>>.>>>>>>>>>.<<.<...<<<<<<.....<<
<<<<<<<..<<<....<<<<<<<....>>>>>>>.....>>>...<<<<.
<<.<<........>>>>>>>>....>>>>>>>>>...<<.......>>..
....>>>>>>......>.>>...<<<<<......<<<....>>>..<<<<
<<<<<.....<<.<<<<<<<.....<<<........>>.>.....>>>>>
...<<<<.<<<<.<......>>>>>.>>>>.....>>>>...>>>>>>>.
>>..<<<<.<<<<<.....>>>>>.>>>>....<<<......>>>...<<
<<<<<...<<<(((.....<<<<<<......<..........<<<.<<<<
<<<<<<.......<<<<<.<<<...<<.........>>...>>>......
...<<......>>...>>>>>...>>>>>>>>>>>>>..........)))
.>....>>>>>>.>>>...>>>>>>><<<<<<<<<.........>>>>>>
>>>....>>>>>.<.<<<<<<<<.<<......<<<<.<<<<....>>>>>
>>>...>>>>>>>>>>..>.....>>>>>><<.....<<.....<<<<<<
.......>>>>>><<<<.....<<<<<.<<...<<<<<<...<<.....>
>.>>>>>>....((<<<<<<...<<<<..<<<....>>>........<<<
<<..>>>>>...>>>>....>>...<<<<<........>>>>>))<<<<.
<<<<.<<<....<<<....>>>.....((<<<<<<...<<<<.<<<<<<<
.<<<<<.<<<<...[[..>>>>.><...<<<<<....<<<<<<....<<<
.....>>>....>>>>>>.....>>>>>....><<<<<<<......>>>>
>>>>>>>...>>>>>>>.>>>>.........>>>>>>.........>>>.
..>>>>>>>>>>>>..>>.....<<......>>>>>>>.<<<<.....>>
>>..>>>>..<<<<.....<<<<<<<.<<.........<.....<<<<<.
....<..>......>>>>><<.<<<<<<<<<<<....>>>>>..>>>>>>
.>>............<<<<<<<<<..<<<.........>>>..<<<<<<<
....<<<<.....>>>>......>>>>>>>.........<<.<<<<<<..
..<<<.....<<<<....>>>>.....>>>.>>>>..>>>>.<<<<<<..
.....>>>>>>......<<..>>......>>.>>>>>>>..>..>>.>>>
>>>>..>>>>>>....>>....<<<<<........>>>>>....<<<<<.
.<<<........<<<<<.<<<<<<..<<<<<.<<<<<<<<..<<<<<<<<
..>>>>>>>>...<<<<<.....<<<<..<<<<<....>>>>>.......
...))..<<<<<.....>>>>>..>>>>..>>>>>.....>>>>>>>>..
>>>>>.......<<<<<<.<<<<<<....>>>>>>>>...<<<<<<<...
<<<<<<.......>>>>>>.....<<......>>....>>>>>>>....<
<<<.<.<<<.....>>>.>>>>><<<<....>>>.>>>>>.<<...<<<<
<<<..<<<<.))))))>>>>>>>>>>>.....>>..>>>>..>>>>>>>.
........<<<<<<...<<.......>>...>>>>>>.............
..<<<<...<<<<..<.<<<<<<<......>>>>>>>...>.<<<.....
....>>>.....>>>>.......>>>>......<<<<<<<....>>>.>>
>>........>>>.>>>>>....<<<<<<<..<<<<.<.<<<<<......
...........>>>>>.><<<<<...<<<<....<<<<<<<<<<]]..>>
>>>..>>>>>...>>>>..>>>>>.<<<<...<<<<<...........>>
>>>...>>>>.>>>>....>>>>>>>.....<<<<<.<<.<<<......<
<.......<<<....>>>....>>........<<<<.....<<<.<<<<<
.......>>>>>.>>>....>>>>..............>>>>>.>>>>>.
..<<<<<<<.............>>....<<<<<<<<<.<<<....<<<<.
<..<<<<<......>>>>>..>>>>>...>>>....>>>>..>>>>>...
>>>>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8pv2 Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.
• Resolution: 2.63 Å
• Binding residue (original residue number in PDB): G2 K3 K7 A12 R19 T20 K24 S29 L30 D32 K35 R48 R51 A57 K90 R93 R105 R225 K640 K641 K644 Q648 M649 Y651 S652 N653
• Binding residue (residue number reindexed from 1): G1 K2 K6 A11 R18 T19 K23 S28 L29 D31 K34 R47 R50 A56 K89 R92 R104 R224 K460 K461 K464 Q468 M469 Y471 S472 N473

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0043021 ribonucleoprotein complex binding

Biological Process

• GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0000466 maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0006364 rRNA processing
• GO:0042254 ribosome biogenesis
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0030687 preribosome, large subunit precursor
• GO:0070545 PeBoW complex

External links

• PDB: RCSB:8pv2, PDBe:8pv2, PDBj:8pv2
• PDBsum: 8pv2
• PubMed: 37921038
• UniProt: G0SHX6