Structure of PDB 8pv6 Chain LL Binding Site BS01

Receptor Information

>8pv6 Chain LL (length=203) Species: 759272 (Thermochaetoides thermophila DSM 1495)

NNHFRKHWQRRVRCHFDQPGKKVTRRLARRAKAAALAPRPVDKLRPIVRC
PTVKYNRRTRLGRGFTLEELKAAGIPRLLAPTIGIAVDHRRKNLSEESLA
ANVQRLKDYKARLILFPRKSNKPKKADTPKDQQTAETTTSLRTSFGVEQP
LAPGFTEISKSEIPAGIEGGAYRALRKARSDARLVGVREKRAKEKAEAEA
NKK

Ligand information

>8pv6 Chain C1 (length=3100)

agguugaccucggaucagguaggaggacccgcugaacuuaagcauaucaa
uaagcggaggaaaagaaaccaacagggauugcccuaguaacggcgaguga
agcggcaacagcucaaauuugaaagcuggcuucggcccgcguuguaauuu
ggagaggaugcuuugggcgaggcuccuucugaguucccuggaacgggacg
ccacagagggugagagccccguauaguuggaagccaagccuguguaaagc
uccuucgacgagucgaguaguuugggaaugcugcucaaaaugggagguaa
auuucuucuaaagcuaaauaccggccagagaccgauagcgcacaaguaga
gugaucgaaagaugaaaagcacuuugaaaagaggguuaaauagcacguga
aauuguugaaagggaagcgcuugugaccagacuugcgcccggcggaucau
ccgguguucucaccggugcacuccgccgggcucaggccagcaucgguucu
ggcggggggauaaaggcccagggaauguggcuccuccgggaguguuauag
cccuggguguaauacccucgccgggaccgaggaccgcgcucugcaaggau
gcuggcguaauggucaccagcgacccgucuugaaacacggaccaaggagu
caagguuuugcgcgaguguuuggguguaaaacccgcacgcguaaugaaag
ugaacguaggugagagcuucggcgcaucaucgaccgauccugauguauuc
ggauggauuugaguaggagcguuaagccuuggacccgaaagauggugaac
uaugcuuggauagggugaagccagaggaaacucugguggaggcucgcagc
gguucugacgugcaaaucgaucgucaaaucugagcaugggggcgaaagac
uaaucgaaccaucuaguagcugguuaccgccgaaguuuccggauagcagu
gucgaccuucaguuuuaugagagcgaaugauuagggacucgggggcgccu
ucauccauucucuguaagaagcccuuguuacuuaacugaacgugggcgaa
ugucgacacuagugggccauuuuugguaagcagaacuggcgaugcgggau
gaaccgaacgcgggguuaaggugccggaguggacgcucaucagacaccac
aaaaggcguuaguacaucuugacagcaggacgguggccauggaagucgga
auccgcuaaggacuguguaacaacucaccugccgaauguacuagcccuga
aaauggauggcgcucaagcgucccacccauaccccgcccucaggguagaa
acgaugcccugaggaguaggcggccguggaggucagugacgaagccuagg
gcgugagcccgggucgaacggccucuagugcagaucuuggugguaguagc
aaauacuucaaugagaacuugaaggaccgaaguggggaaagguuccaugu
gaacagcgguuggacauggguuagucgauccuaagccauagggaaguucc
guuucaaaggggcacucgugccccgggcgaaagggaagccgguuaauauu
ccggcaccuggauguggguuuugcgcggcaacgcaacugaacgcggagac
gacggcgggggccccgggcagaguucucuuuucuucuuaacggucuauca
cccuggaaacaguuugucuggagauaggguuuaauggccggaagagcccg
acacuucugucggguccggugcgcucucgacgucccuugaaaauccgcgg
gagggaauaauucucacgccaggucguacucauaaccgcagcaggucccc
aaggugaacagccucugguugauagaacaauguagauaagggaagucggc
aaaauagauccguaacuucgggaaaaggauuggcucuaaggguugggcac
gugcgugcgguuaacaaccaacuuagaacugguacggacagggggaaucu
gacugucuaauuaaaacauagcauugcgauggccagaaagugguguugac
gcaaugugauuucgcccagugcucuaugucaaagugaagaaauucaacca
agcgcggguaaacggcgggaguaacuaugacucucuuaagguuaacgaga
uucccacugucccuaucuacuaucuagcgaaaccacagccaagggaacgg
gcuuggcaaaaucagcggggaaagaagacccuguugagcuugacucuagu
uugacauugugaaaagacauaggagguguagaauaggugggagcuucggc
gccagugaaauaccacuacuccuauuguuuuuuuacuuauucaaugaagc
ggggcuggacuugcguccaacuucuggaguuaagguccuucgcgggccga
cccggguugaagacauugucagguggggaguuugggcacaucugcaggug
uccuaaggggggcucauggagaacagaaaucuccaguagaacaaaagggu
aaaaguccccuugauuuugauuuuugugaauacaaaccaugaaagugugg
ccccuuuagucccucgaaauuugaggcuagaggaaguuaccacagggaug
gcuuguggcggccaagcguucauagcgacgucgcuuugauccuucgaugu
cggcucuuccuaucauaccgaagcagaauucgguaagcguuggauuguac
ccacuaauagggaacgagcuggguuuagaccgucgugagacagguuaguu
uuacccuacugaugaacucgucgcaaugguaauucagcuuaguacgagag
gaaccgcugauucagauaauugguuuuugcgguuguccgaccgggcagug
ccgcgaagcuaccaucugcuggauaauggcugaacgccucuaagucagaa
uccaugccagaacgcgacgauacuacccgcacguuguagacguauaagaa
uaggcuccggccucguauccuagcaggcgauuccuccgccggccucgaag
uggccgucgguaauucgcguauugcaauuuagacacgcgcgggaucaaau
ccuuugcagacgacuuagaugugcgaaaggguccuguaagcaguagagua
gccuuguuguuacgaucugcugaggguaagcccuccuucgccuagauuuc

...........................<<<<<<.....<......>....
..>>>>>.>...<.....<<....>>..<<<<<......<<.....>>..
...>>>>>..<<<..<<.......<<.<<<....>>>.>>.......>>.
...<<<<<.<<<<<<<<<..<<<<<<..<<<...<<<<......>>>>.(
(......<<<.....))>>>.>..>>..>>>.>>>..>>>>....>>>>>
>>>.>>........<<<<<<<........>>>>>>>.....<<<<<..((
((((>>>>>..>>>....>.............................<<
....>>...............<<<<....>>>>.................
.................<<<<.<<<<<<.<...<<.<<<<<<<<<.....
<<<<<<....>>>>>>......>>>>>>>>>.>>.<<<<<<<.<<<<<<<
<<<<<<<<.......<<<<<<<<......<<<<<....>>>>>.......
>>>>>>>>......>>>>>>>>>>>>>>>........<<...>>.....>
>>>>>>....>>>>>>>.>>>>..<<<<........>>>><<<<<<...<
<<<<<<<<.<<<<..<<<..<<<<<.....>>>>>..>>>...<<....>
>.......<<<<<..<<....>>...>>>>>.<<<<<<<<...<<....>
>...>>>>.>>.>>....>>>>.>>>>>>>>>.<<.<...<<<<<<....
.<<<<<<<<<..<<<....<<<<<<<....>>>>>>>.....>>>...<<
<<.<<.<<........>>>>>>>>....>>>>>>>>>...<<.......>
>......>>>>>>......>.>>...<<<<<......<<..>>..<<<<<
<<<<.....<<.<<<<<<<.........<<....<<<...<<<<<..>>>
>>.>>>..>>..>>>>>...<<<<.<<<<.<......>>>>>.>>>>.>>
>>.>>>>>>>.>>..<<<<.<<<<<.....>>>>>.>>>>....<<<...
...>>>...<<<<<<<...<<<(((.....<<<<<<.....<<.......
...<<<.<<<<<<<<<<.......<<<<<.<<<...<<.........>>.
..>>>.........<<......>>...>>>>>...>>>>>>>>>>>>>..
........))).>>...>>>>>>.>>>...>>>>>>><<<<<<<<<....
.....>>>>>>>>>....>>>>>.<.<<<<<<<<.<<......<<<<.<<
<<....>>>>>>>>...>>>>>>>>>>..>.....>>>>>><<.....<<
.....<<<<<<.......>>>>>><<<<.....<<<<<.<<...<<<<<<
...<<.....>>.>>>>>>....((<<<<<<...<<<...<<<....>>>
........<<<<<......>>>>>.>>>....>>...<<<<<........
>>>>>))<<<<.<<<<.<<<....<<<....>>>...<..{<<<<<<...
<<<<.<<<<<<<.<<<<<.<<<<...[[..>>>>.><...<<<<<....<
<<<<<....<<<.....>>>....>>>>>>.....>>>>>....><<<<<
<<......>>>>>>>>>>>...>>>>>>>.>>>>.........>>>>>>.
..>.....>>>...>>>>>>>>>>>>..>>.....<<......>>>>>>>
.<<<<.....>>>>..>>>>..<<<<.....<<<<<<<.<<.........
<.....<<<<<....<....>.....>>>>><<.<<<<<<<<<<<.<<<<
<..>>>>>......>>>>>..>>>>>>.>>............<<<<<<<<
<..<<<.........>>>..<<<<<<<....<<<<.....>>>>......
>>>>>>>......<<<..<<<<<<..<<<.....<<<<....>>>>....
.>>>.>>>>..>>>>><<<<<<.......>>>>>>..........>>.>>
>>>>>..>..>>.>>>>>>>..>>>>>>....>>....<<<<<.......
.>>>>>....<<<<<..<<<........<<<<<.<<<<<<..<<<<<.<<
<<<<<<..<<<<<<<<<<<<<<<<<..........<<<<<..<<....>>
............>>>>>.>>>>>>>.>>>>>>>>>>...<<<<<.....<
<<<..<<<<<....>>>>>..........}...<<<<<.....>>>>>..
>>>>..>>>>>.....>>>>>>>>..>>>>>...<<.<<<<<<..>>>>>
>>>...<<<<<<<...<<<<<<.......>>>>>>.....<<....((>>
....>>>>>>>...<<<.<<<<<....>>>>.>>>>.<<<....>>>...
))<<<<<<<..<<<<.))))))>>>>>>>>>>>.>>>>..>>>>>>>...
......<<<<<<...<<.......>>...>>>>>>...............
<<<<...<<<<..<.<<<<<<<......>>>>>>>...>.<<<.<...>.
>>>.....>>>>.....>>>>......<<<<<<<....>>>.>>>>....
....>>>.>>>>>....<<<<<<<..<<<<.<.<<<<<............
.....>>>>>.><<<<<...<<<<....<<<<<<<<<<]]..>>>>>..>
>>>>...>>>>..>>>>>.<<<<...<<<<<...........>>>>>...
>>>>.>>>>....>>>>>>>.....<<<<<.<<.<<<......<<.....
..<<<....>>>....>>........<<<<.....<<<.<<<<<......
.>>>>>.>>>....>>>>..............>>>>>.>>>>>...<<<<
<<<.............>>....<<<<<<<<<.<<<....<<<<....<<<
<<......>>>>>...>>>>...>>>....>>>>..>>>>>...>>>>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8pv6 Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.
• Resolution: 2.94 Å
• Binding residue (original residue number in PDB): H13 F14 R15 K16 H17 W18 R23 Q28 P29 K31 K32 R35 R36 R39 K42 K53 R59 P61 T62 Y65 N66 R68 R70 G72 R73 K81 R87 D98 H99 R100 R101 K102 S105 R128 K129 S130 N131 K132 K134 K135 R152 Y182 R183 R186 R189 D191 R193 L194 R198 K200 R201
• Binding residue (residue number reindexed from 1): H3 F4 R5 K6 H7 W8 R13 Q18 P19 K21 K22 R25 R26 R29 K32 K43 R49 P51 T52 Y55 N56 R58 R60 G62 R63 K71 R77 D88 H89 R90 R91 K92 S95 R118 K119 S120 N121 K122 K124 K125 R142 Y172 R173 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:8pv6, PDBe:8pv6, PDBj:8pv6
• PDBsum: 8pv6
• PubMed: 37921038
• UniProt: G0S992