Structure of PDB 8pv2 Chain LS Binding Site BS01

Receptor Information

>8pv2 Chain LS (length=174) Species: 759272 (Thermochaetoides thermophila DSM 1495)

MGRLQEYQVIGRHLPTEANPNPALYRMRIFAPNEVVAKSRFWYFLRGLKK
VKKATGEIVSVNVISEKHPLKVKNFGIWLRYDSRSGTHNMYKEYRETSRV
AAVEAMYADMAARHRARFRSIHILKVVELEKTEDVKRPYIKQLVAKNLSF
PLPHRVPKISTKKIFSAKRPSTFS

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): M1 G2 N62 S65 E66 K67 H68 K71 Y81 R84 S85 H88 Y91 K92 A111 A112 R113 H114 R115 R117 T132 R137 Y139 V144 A145 K146 P153 H154 T161 K163 A167 P170 T172 F173 S174
• Binding residue (residue number reindexed from 1): M1 G2 N62 S65 E66 K67 H68 K71 Y81 R84 S85 H88 Y91 K92 A111 A112 R113 H114 R115 R117 T132 R137 Y139 V144 A145 K146 P153 H154 T161 K163 A167 P170 T172 F173 S174

Gene Ontology

Molecular Function

• 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:8pv2, PDBe:8pv2, PDBj:8pv2
• PDBsum: 8pv2
• PubMed: 37921038
• UniProt: G0SCE2