Structure of PDB 8pv8 Chain CK Binding Site BS01

Receptor Information

>8pv8 Chain CK (length=233) Species: 759272 (Thermochaetoides thermophila DSM 1495)

PQNEYIERHRKLHGRRLDAEERARKKAAREGHKNSENAQNLRGLRAKLYA
KQRHAQKIQMRKAIKQHEERNVEPSDPIPSYLLDRAARFSVPIPKVRGIS
EEEMFKVVKTGKKTHKKGWKRIVTKPTFVGPDFTRRPVKYERFIRPMGLR
YKKANVTHPTLNVTVQLPILSVKKNPSNPLYTQLGVLTKGTIIEVNVSDL
GIVTASGKIAWGRYAQITNNPENDGCVNAVLLV

Ligand information

>8pv8 Chain C1 (length=3085)

uugaccucggaucagguaggaggacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaacagggauugcccuaguaacggcgagugaagc
ggcaacagcucaaauuugaaagcuggcuucggcccgcguuguaauuugga
gaggaugcuuugggcgaggcuccuucugaguucccuggaacgggacgcca
cagagggugagagccccguauaguuggaagccaagccuguguaaagcucc
uucgacgagucgaguaguuugggaaugcugcucaaaaugggagguaaauu
ucuucuaaagcuaaauaccggccagagaccgauagcgcacaaguagagug
aucgaaagaugaaaagcacuuugaaaagaggguuaaauagcacgugaaau
uguugaaagggaagcgcuugugaccagacuugcgcccggcggaucauccg
guguucucaccggugcacuccgccgggcucaggccagcaucgguucuggc
ggggggauaaaggcccagggaauguggcuccuccgggaguguuauagccc
uggguguaauacccucgccgggaccgaggaccgcgcucugcaaggaugcu
ggcguaauggucaccagcgacccgucuugaaacacggaccaaggagucaa
gguuuugcgcgaguguuuggguguaaaacccgcacgcguaaugaaaguga
acguaggugagagcuucggcgcaucaucgaccgauccugauguauucgga
uggauuugaguaggagcguuaagccuuggacccgaaagauggugaacuau
gcuuggauagggugaagccagaggaaacucugguggaggcucgcagcggu
ucugacgugcaaaucgaucgucaaaucugagcaugggggcgaaagacuaa
ucgaaccaucuaguagcugguuaccgccgaaguuuccggauagcaguguc
gaccuucaguuuuaugagagcgaaugauuagggacucgggggcgccuuca
uccauucucuguaagaagcccuuguuacuuaacugaacgugggcgaaugu
cgacacuagugggccauuuuugguaagcagaacuggcgaugcgggaugaa
ccgaacgcgggguuaaggugccggaguggacgcucaucagacaccacaaa
aggcguuaguacaucuugacagcaggacgguggccauggaagucggaauc
cgcuaaggacuguguaacaacucaccugccgaauguacuagcccugaaaa
uggauggcgcucaagcgucccacccauaccccgcccucaggguagaaacg
augcccugaggaguaggcggccguggaggucagugacgaagccuagggcg
ugagcccgggucgaacggccucuagugcagaucuuggugguaguagcaaa
uacuucaaugagaacuugaaggaccgaaguggggaaagguuccaugugaa
cagcgguuggacauggguuagucgauccuaagccauagggaaguuccguu
ucaaaggggcacucgugccccguguggcgaaagggaagccgguuaauauu
ccggcaccuggauguggguuuugcgcggcaacgcaacugaacgcggagac
gacggcgggggccccgggcagaguucucuuuucuucuuaacggucuauca
cccuggaaacaguuugucuggagauaggguuuaauggccggaagagcccg
acacuucugucggguccggugcgcucucgacgucccuugaaaauccgcgg
gagggaauaauucucacgccaggucguacucauaaccgcagcaggucccc
aaggugaacagccucugguugauagaacaauguagauaagggaagucggc
aaaauagauccguaacuucgggaaaaggauuggcucuaaggguugguaac
aaccaacuuagaacugguacggacagggggaaucugacugucuaauuaaa
acauagcauugcgauggccagaaagugguguugacgcaaugugauuucgc
ccagugcucuaugucaaagugaagaaauucaaccaagcgcggguaaacgg
cgggaguaacuaugacucucuuaagguuaacgagauucccacugucccua
ucuacuaucuagcgaaaccacagccaagggaacgggcuuggcaaaaucag
cggggaaagaagacccuguugagcuugacucuaguuugacauugugaaaa
gacauaggagguguagaauaggugggagcuucggcgccagugaaauacca
cuacuccuauuguuuuuuuacuuauucaaugaagcggggcuggacuugcg
uccaacuucuggaguuaagguccuucgcgggccgacccggguugaagaca
uugucagguggggaguuugggcacaucugcagguguccuaaggggggcuc
auggagaacagaaaucuccaguagaacaaaaggguaaaaguccccuugau
uuugauuuuugugaauacaaaccaugaaaguguggccccuuuagucccuc
gaaauuugaggcuagaggaaguuaccacagggauggcuuguggcggccaa
gcguucauagcgacgucgcuuugauccuucgaugucggcucuuccuauca
uaccgaagcagaauucgguaagcguuggauuguacccacuaauagggaac
gagcuggguuuagaccgucgugagacagguuaguuuuacccuacugauga
acucgucgcaaugguaauucagcuuaguacgagaggaaccgcugauucag
auaauugguuuuugcgguuguccgaccgggcagugccgcgaagcuaccau
cugcuggauaauggcugaacgccucuaagucagaauccaugccagaacgc
gacgauacuacccgcacguuguagacguauaagaauaggcuccggccucg
uauccuagcaggcgauuccuccgccggccucgaaguggccgucgguaauu
cgcguauugcaauuuagacacgcgcgggaucaaauccuuugcagacgacu
uagaugugcgaaaggguccuguaagcaguagaguagccuuguuguuacga
ucugcugaggguaagcccuccuucgccuagauuuc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8pv8 Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.
• Resolution: 2.91 Å
• Binding residue (original residue number in PDB): P2 E5 Y6 I7 E8 R23 R25 K26 A29 R30 H33 K34 S36 A39 Q40 L42 R43 G44 L45 R46 K48 L49 A51 R54 H55 K58 I59 K123 R125 V135 V136 K137 T138 G139 K140 K141 T142 H143 K145 W147 R163 V166 I172 R173 P174 M175 G176 N183 T192 Q194 T232 A233 S234 D252 N256
• Binding residue (residue number reindexed from 1): P1 E4 Y5 I6 E7 R22 R24 K25 A28 R29 H32 K33 S35 A38 Q39 L41 R42 G43 L44 R45 K47 L48 A50 R53 H54 K57 I58 K95 R97 V107 V108 K109 T110 G111 K112 K113 T114 H115 K117 W119 R135 V138 I144 R145 P146 M147 G148 N155 T164 Q166 T204 A205 S206 D224 N228

Gene Ontology

Biological Process

• GO:0000460 maturation of 5.8S rRNA
• GO:0000470 maturation of LSU-rRNA
• GO:0006364 rRNA processing
• GO:0042254 ribosome biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0030687 preribosome, large subunit precursor
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8pv8, PDBe:8pv8, PDBj:8pv8
• PDBsum: 8pv8
• PubMed: 37921038
• UniProt: G0S081