Structure of PDB 8pv4 Chain LG Binding Site BS01

Receptor Information

>8pv4 Chain LG (length=235) Species: 759272 (Thermochaetoides thermophila DSM 1495)

PKNPLLEKRPRNFGIGQDIQPKRNLSRMVKWPEYIRLQRQKKILRMRLKV
PPAIAQFQYTLDKNLAAQAFKLLNKYRPETKQEKKERLLREATAIKEGKK
KEDVSKKPYTVKYGLNHVVGLIENKKASLVLIANDVDPIELVVFLPALCR
KMGIPYAIIKGKARLGTLVHKKTAAVVAITEVRSEDKNELAKLISAVKEG
YLEKVEDTRKRWGGGIMGFKAQKREEKRKKSLETA

Ligand information

>8pv4 Chain C1 (length=3136)

agguugaccucggaucagguaggaggacccgcugaacuuaagcauaucaa
uaagcggaggaaaagaaaccaacagggauugcccuaguaacggcgaguga
agcggcaacagcucaaauuugaaagcuggcuucggcccgcguuguaauuu
ggagaggaugcuuugggcgaggcuccuucugaguucccuggaacgggacg
ccacagagggugagagccccguauaguuggaagccaagccuguguaaagc
uccuucgacgagucgaguaguuugggaaugcugcucaaaaugggagguaa
auuucuucuaaagcuaaauaccggccagagaccgauagcgcacaaguaga
gugaucgaaagaugaaaagcacuuugaaaagaggguuaaauagcacguga
aauuguugaaagggaagcgcuugugaccagacuugcgcccggcggaucau
ccgguguucucaccggugcacuccgccgggcucaggccagcaucgguucu
ggcggggggauaaaggcccagggaauguggcuccuccgggaguguuauag
cccuggguguaauacccucgccgggaccgaggaccgcgcucugcaaggau
gcuggcguaauggucaccagcgacccgucuugaaacacggaccaaggagu
caagguuuugcgcgaguguuuggguguaaaacccgcacgcguaaugaaag
ugaacguaggugagagcuucggcgcaucaucgaccgauccugauguauuc
ggauggauuugaguaggagcguuaagccuuggacccgaaagauggugaac
uaugcuuggauagggugaagccagaggaaacucugguggaggcucgcagc
gguucugacgugcaaaucgaucgucaaaucugagcaugggggcgaaagac
uaaucgaaccaucuaguagcugguuaccgccgaaguuucccucaggauag
cagugucgaccuucaguuuuaugagguaaagcgaaugaacuuuaaauaug
uaagaagcccuuguuacuuaacugaacgugggcauucgaauguaucgaca
cuagugggccauuuuugguaagcagaacuggcgaugcgggaugaaccgaa
cgcgggguuaaggugccggaguggacgcucaucagacaccacaaaaggcg
uuaguacaucuugacagcaggacgguggccauggaagucggaauccgcua
aggacuguguaacaacucaccugccgaauguacuagcccugaaaauggau
ggcgcucaagcgucccacccauaccccgcccucaggguagaaacgaugcc
cugaggaguaggcggccguggaggucagugacgaagccuagggcgugagc
ccgggucgaacggccucuagugcagaucuuggugguaguagcaaauacuu
caaugagaacuugaaggaccgaaguggggaaagguuccaugugaacagcg
guuggacauggguuagucgauccuaagccauagggaaguuccguuucaaa
ggggcacucgugccccguguggcgaaagggaagccgguuaauauuccggc
accuggauguggguuuugcgcggcaacgcaacugaacgcggagacgacgg
cgggggccccgggcagaguucucuuuucuucuuaacggucuaucacccug
gaaacaguuugucuggagauaggguuuaauggccggaagagcccgacacu
ucugucggguccggugcgcucucgacgucccuugaaaauccgcgggaggg
aauaauucucacgccaggucguacucauaaccgcagcagguccccaaggu
gaacagccucugguugauagaacaauguagauaagggaagucggcaaaau
agauccguaacuucgggaaaaggauuggcucuaaggguugggcacgugcg
ugcgguuaacaaccaacuuagaacugguacggacagggggaaucugacug
ucuaauuaaaacauagcauugcgauggccagaaagugguguugacgcaau
gugauuucugcccagugcucugaaugucaaagugaagaaauucaaccaag
cgcggguaaacggcgggaguaacuaugacucucuguagccaaauggauua
acgagauucccacugucccuaucuacuaucuagcgaaaccacagccaagg
gaacgggcuuggcaaaaucagcggggaaagaagacccuguugagcuugac
ucuaguuugacauugugaaaagacauaggagguguagaauaggugggagc
uucggcgccagugaaauaccacuacuccuauuguuuuuuuacuuauucaa
ugaagcggggcuggacuugcguccaacuucuggaguuaagguccuucgcg
ggccgacccggguugaagacauugucagguggggaguuuggcuggggcgg
cacaucugugcagguguccuaaggggggcucauggagaacagaaaucucc
aguagaacaaaaggguaaaaguccccuugauuuugauuuucagugugaau
acaaaccaugaaaguguggccuaucgauccuuuagucccucgaaauuuga
ggcuagaggugccagaaaaguuaccacagggauggcuuguggcggccaag
cguucauagcgacgucgcuuugauccuucgaugucggcucuuccuaucau
accgaagcagaauucgguaagcguuggauuguucacccacuaauagggaa
cgagcuggguuuagaccgucgugagacagguuaguuuuacccuacugaug
aacucgucgcaaugguaauucagcuuaguacgagaggaaccgcugauuca
gauaauugguuuuugcgguuguccgaccgggcagugccgcgaagcuacca
ucugcuggauaauggcugaacgccucuaagucagaauccaugccagaacg
cgacgauacuacccgcacguuguagacguauaagaauaggcuccggccuc
guauccuagcaggcgauuccuccgccggccucgaaguggccgucgguaau
ucgcguauugcaauuuagacacgcgcgggaucaaauccuuugcagacgac
uuagaugugcgaaaggguccuguaagcaguagaguagccuuguuguuacg
aucugcugaggguaagcccuccuucgccuagauuuc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8pv4 Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): K26 E31 K32 R33 R35 F37 G38 I39 Q41 Q44 P45 K46 R47 R51 M52 K54 Y58 R60 K66 L68 M70 R71 L72 K73 E103 K108 R111 S129 K130 K131 P132 K136 Y137 G138 L139 H141 G144 L145 N148 D161 L165 K186 A187 K195 K196 A199 G242 F243 K244 A245 K247 R248 R252
• Binding residue (residue number reindexed from 1): K2 E7 K8 R9 R11 F13 G14 I15 Q17 Q20 P21 K22 R23 R27 M28 K30 Y34 R36 K42 L44 M46 R47 L48 K49 E79 K84 R87 S105 K106 K107 P108 K112 Y113 G114 L115 H117 G120 L121 N124 D137 L141 K162 A163 K171 K172 A175 G218 F219 K220 A221 K223 R224 R228

Gene Ontology

Molecular Function

• GO:0003723 RNA binding

Biological Process

• GO:0000470 maturation of LSU-rRNA
• GO:0042254 ribosome biogenesis

Cellular Component

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

External links

• PDB: RCSB:8pv4, PDBe:8pv4, PDBj:8pv4
• PDBsum: 8pv4
• PubMed: 37921038
• UniProt: G0SAJ9