Structure of PDB 8pvl Chain LR Binding Site BS01

Receptor Information

>8pvl Chain LR (length=155) Species: 759272 (Thermochaetoides thermophila DSM 1495)

VNLRTQKRLAASVLGCGEGKVWLDPNEVSEISNANSRQSIRKLVADGLII
KKPVTMHSRSRARELNLARRIGRHRGFGKRKGTADARMPQQVLWMRRQRV
LRRLLVKYRASGKIDKHLYHELYHLAKGNTFKHKRALVEHIHRAKAEKAR
ERQIK

Ligand information

>8pvl Chain C1 (length=3078)

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
ucuaguuugacauugugaaaagauuuuuuuacuuauucaaugaagcgggg
cuggacuugcguccaacuucuggaguuaagguccuucgcgggccgacccg
gguugaagacauugucagguggggaguuuggcuggggcggcacaucugug
cagguguccuaaggggggcucauggagaacagaaaucuccaguagaacaa
aaggguaaaaguccccuugauuuugauuuucagugugaauacaaaccaug
aaaguguggccuaucgauccuuuagucccucgaaauuugaggcuagaggu
gccagaaaaguuaccacagggauggcuuguggcggccaagcguucauagc
gacgucgcuuugauccuucgaugucggcucuuccuaucauaccgaagcag
aauucgguaagcguuggauuguucacccacuaauagggaacgugagcugg
guuuagaccgucgugagacagguuaguuuuacccuacugaugaacucguc
gcaaugguaauucagcuuaguacgagaggaaccgcugauucagauaauug
guuuuugcgguuguccgaccgggcagugccgcgaagcuaccaucugcugg
auaauggcugaacgccucuaagucagaauccaugccagaacgcgacgaua
cuacccgcacguuguagacguauaagaauaggcuccggccucguauccua
gcaggcgauuccuccgccggccucgaaguggccgucgguaauucgcguau
ugcaauuuagacacgcgcgggaucaaauccuuugcagacgacuuagaugu
gcgaaaggguccuguaagcaguagaguagccuuguuguuacgaucugcug
aggguaagcccuccuucgccuagauuuc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8pvl Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.
• Resolution: 2.19 Å
• Binding residue (original residue number in PDB): V2 N3 R5 T6 K8 R9 L10 G18 E19 K21 W23 L24 P26 S37 R38 R42 T56 M57 H58 S59 R60 S61 R62 R64 R70 R71 R74 H75 R76 G77 F78 G79 K80 R81 K82 G83 T84 A87 R88 M89 P90 V93 W95 M96 R97 R100 R103 R104 R110 S112 G113 K114 K117 H118 Y120 H121 Y124 H125 K128 G129 N130 H134 K135 R136 H143 K146
• Binding residue (residue number reindexed from 1): V1 N2 R4 T5 K7 R8 L9 G17 E18 K20 W22 L23 P25 S36 R37 R41 T55 M56 H57 S58 R59 S60 R61 R63 R69 R70 R73 H74 R75 G76 F77 G78 K79 R80 K81 G82 T83 A86 R87 M88 P89 V92 W94 M95 R96 R99 R102 R103 R109 S111 G112 K113 K116 H117 Y119 H120 Y123 H124 K127 G128 N129 H133 K134 R135 H142 K145

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019887 protein kinase regulator activity

Biological Process

• GO:0006412 translation
• GO:0006417 regulation of translation
• GO:0034198 cellular response to amino acid starvation

Cellular Component

• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8pvl, PDBe:8pvl, PDBj:8pvl
• PDBsum: 8pvl
• PubMed: 37921038
• UniProt: G0S9T3