Structure of PDB 8pv5 Chain LL Binding Site BS01

Receptor Information

>8pv5 Chain LL (length=203) Species: 759272 (Thermochaetoides thermophila DSM 1495)

NNHFRKHWQRRVRCHFDQPGKKVTRRLARRAKAAALAPRPVDKLRPIVRC
PTVKYNRRTRLGRGFTLEELKAAGIPRLLAPTIGIAVDHRRKNLSEESLA
ANVQRLKDYKARLILFPRKSNKPKKADTPKDQQTAETTTSLRTSFGVEQP
LAPGFTEISKSEIPAGIEGGAYRALRKARSDARLVGVREKRAKEKAEAEA
NKK

Ligand information

>8pv5 Chain C1 (length=3060)

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
gcacucgugccccguguggcgaaagggaagccgguuaauauuccggcacc
uggauguggguuuugcgcggcaacgcaacugaacgcggagacgacggcgg
gggccccgggcagaguucucuuuucuucuuaacggucuaucacccuggaa
acaguuugucuggagauaggguuuaauggccggaagagcccgacacuucu
gucggguccggugcgcucucgacgucccuugaaaauccgcgggagggaau
aauucucacgccaggucguacucauaaccgcagcagguccccaaggugaa
cagccucugguugauagaacaauguagauaagggaagucggcaaaauaga
uccguaacuucgggaaaaggauuggcucuaaggguugguaacaaccaacu
uagaacugguacggacagggggaaucugacugucuaauuaaaacauagca
uugcgauggccagaaagugguguugacgcaaugugauuucugcccagugc
ucugaaugucaaagugaagaaauucaaccaagcgcggguaaacggcggga
guaacuaugacucucuguagccaaauggauuaacgagauucccacugucc
cuaucuacuaucuagcgaaaccacagccaagggaacgggcuuggcaaaau
cagcggggaaagaagacccuguugagcuugacucuaguuugacauuguga
aaagauuuuuuuacuuauucaaugaagcggggcuggacuugcguccaacu
ucuggaguuaagguccuucgcgggccgacccggguugaagacauugucag
guggggaguuuggcuggggcggcacaucugugcagguguccuaagggggg
cucauggagaacagaaaucuccaguagaacaaaaggguaaaaguccccuu
gauuuugauuuucagugugaauacaaaccaugaaaguguggccuaucgau
ccuuuagucccucgaaauuugaggcuagaggugccagaaaaguuaccaca
gggauggcuuguggcggccaagcguucauagcgacgucgcuuugauccuu
cgaugucggcucuuccuaucauaccgaagcagaauucgguaagcguugga
uuguucacccacuaauagggaacgugagcuggguuuagaccgucgugaga
cagguuaguuuuacccuacugaugaacucgucgcaaugguaauucagcuu
aguacgagaggaaccgcugauucagauaauugguuuuugcgguuguccga
ccgggcagugccgcgaagcuaccaucugcuggauaauggcugaacgccuc
uaagucagaauccaugccagaacgcgacgauacuacccgcacguuguaga
cguauaagaauaggcuccggccucguauccuagcaggcgauuccuccgcc
ggccucgaaguggccgucgguaauucgcguauugcaauuuagacacgcgc
gggaucaaauccuuugcagacgacuuagaugugcgaaaggguccuguaag
caguagaguagccuuguuguuacgaucugcugaggguaagcccuccuucg
ccuagauuuc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8pv5 Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.
• Resolution: 2.86 Å
• Binding residue (original residue number in PDB): H13 F14 R15 K16 H17 W18 R20 F26 Q28 P29 K31 K32 R35 R36 R39 K42 R59 P61 T62 Y65 N66 R68 R70 G72 R73 L77 K81 R87 D98 H99 R100 R101 K102 S105 K129 S130 N131 K132 K134 R152 Y182 R186 R189 D191 R193 L194 R198 K200 R201
• Binding residue (residue number reindexed from 1): H3 F4 R5 K6 H7 W8 R10 F16 Q18 P19 K21 K22 R25 R26 R29 K32 R49 P51 T52 Y55 N56 R58 R60 G62 R63 L67 K71 R77 D88 H89 R90 R91 K92 S95 K119 S120 N121 K122 K124 R142 Y172 R176 R179 D181 R183 L184 R188 K190 R191

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:8pv5, PDBe:8pv5, PDBj:8pv5
• PDBsum: 8pv5
• PubMed: 37921038
• UniProt: G0S992