Structure of PDB 8pv3 Chain LS Binding Site BS01

Receptor Information

>8pv3 Chain LS (length=174) Species: 759272 (Thermochaetoides thermophila DSM 1495)

MGRLQEYQVIGRHLPTEANPNPALYRMRIFAPNEVVAKSRFWYFLRGLKK
VKKATGEIVSVNVISEKHPLKVKNFGIWLRYDSRSGTHNMYKEYRETSRV
AAVEAMYADMAARHRARFRSIHILKVVELEKTEDVKRPYIKQLVAKNLSF
PLPHRVPKISTKKIFSAKRPSTFS

Ligand information

>8pv3 Chain C1 (length=2998)

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
gugauuucguagccaaauggauuaacgagauucccacugucccuaucuac
uaucuagcgaaaccacagccaagggaacgggcuuggcaaaaucagcgggg
aaagaagacccuguugagcuugacucuaguuugacauugugaaaauuuuu
acuuauucaaugaagcggggcuggacuugcguccaacuucuggaguuaag
guccuucgcgggccgacccggguugaagacauugucagguggggaguuug
gcuggggcggcacaucugugcagguguccuaaggggggcucauggagaac
agaaaucuccaguagaacaaaaggguaaaaguccccuugauuuugauuuu
cagugugaauacaaaccaugaaaguguggccuaucgauccuuuagucccu
cgaaauuugaggcuagaggugccagaaaaguuaccacagggauggcuugu
ggcggccaagcguucauagcgacgucgcuuugauccuucgaugucggcuc
uuccuaucauaccgaagcagaauucgguaagcguuggauuguucacccac
uaauagggaacgugagcuggguuuagaccgucgugagacagguuaguuuu
acccuacugaugaacucgucgcaaugguaauucagcuuaguacgagagga
accgcugauucagauaauugguuuuugcgguuguccgaccgggcagugcc
gcgaagcuaccaucugcuggauaauggcugaacgccucuaagucagaauc
caugccagaacgcgacgauacuacccgcacguuguagacguauaagaaua
ggcuccggccucguauccuagcaggcgauuccuccgccggccucgaagug
gccgucgguaauucgcguauugcaauuuagacacgcgcgggaucaaaucc
uuugcagacgacuuagaugugcgaaaggguccuguaagcaguagaguagc
cuuguuguuacgaucugcugaggguaagcccuccuucgccuagauuuc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8pv3 Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): M1 G2 N62 S65 E66 K67 H68 K71 Y81 S83 R84 S85 H88 N89 M90 Y91 K92 A111 A112 R113 H114 R115 R117 T132 R137 Y139 V144 K146 P153 H154 T161 K163 A167 K168 P170 T172 F173 S174
• Binding residue (residue number reindexed from 1): M1 G2 N62 S65 E66 K67 H68 K71 Y81 S83 R84 S85 H88 N89 M90 Y91 K92 A111 A112 R113 H114 R115 R117 T132 R137 Y139 V144 K146 P153 H154 T161 K163 A167 K168 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:8pv3, PDBe:8pv3, PDBj:8pv3
• PDBsum: 8pv3
• PubMed: 37921038
• UniProt: G0SCE2