Structure of PDB 8pvk Chain LQ Binding Site BS01

Receptor Information

>8pvk Chain LQ (length=150) Species: 759272 (Thermochaetoides thermophila DSM 1495)

GIDLRWKHVRSSHRKAPKSDNVYLKLLVKLYRFLARRTEAPFNKVVLRRL
FMSRINRPPVSLSRIARNLKNGNEKKTVVVVATVTDDNRLLQVPKMEVAA
LRFTAKARARIEAAGGRTLTLDQLALEKPTGANTLLLRGPKNAREAVKHF

Ligand information

>8pvk Chain C1 (length=3138)

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
ucuaguuugacauugugaaaagacauaggagguguagaauaggugggagc
uucggcgccagugaaauaccacuacuccuauuguuuuuuuacuuauucaa
ugaagcggggcuggacuugcguccaacuucuggaguuaagguccuucgcg
ggccgacccggguugaagacauugucagguggggaguuuggcuggggcgg
cacaucugugcagguguccuaaggggggcucauggagaacagaaaucucc
aguagaacaaaaggguaaaaguccccuugauuuugauuuucagugugaau
acaaaccaugaaaguguggccuaucgauccuuuagucccucgaaauuuga
ggcuagaggugccagaaaaguuaccacagggauggcuuguggcggccaag
cguucauagcgacgucgcuuugauccuucgaugucggcucuuccuaucau
accgaagcagaauucgguaagcguuggauuguucacccacuaauagggaa
cgugagcuggguuuagaccgucgugagacagguuaguuuuacccuacuga
ugaacucgucgcaaugguaauucagcuuaguacgagaggaaccgcugauu
cagauaauugguuuuugcgguuguccgaccgggcagugccgcgaagcuac
caucugcuggauaauggcugaacgccucuaagucagaauccaugccagaa
cgcgacgauacuacccgcacguuguagacguauaagaauaggcuccggcc
ucguauccuagcaggcgauuccuccgccggccucgaaguggccgucggua
auucgcguauugcaauuuagacacgcgcgggaucaaauccuuugcagacg
acuuagaugugcgaaaggguccuguaagcaguagaguagccuuguuguua
cgaucugcugaggguaagcccuccuucgccuagauuuc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8pvk Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.
• Resolution: 2.55 Å
• Binding residue (original residue number in PDB): G31 W36 K37 H38 V39 R40 S41 S42 H43 R44 S49 K59 F63 R66 P71 R78 M82 S83 R84 I85 N86 S91 S93 R94 R97 K100 N101 N103 K106 T113 T115 D116 D117 N118 R119 R132 T134 A135 G161 A162 N163 R168 G169 K171 N172 A173 R174 E175 A176 K178 H179 F180
• Binding residue (residue number reindexed from 1): G1 W6 K7 H8 V9 R10 S11 S12 H13 R14 S19 K29 F33 R36 P41 R48 M52 S53 R54 I55 N56 S61 S63 R64 R67 K70 N71 N73 K76 T83 T85 D86 D87 N88 R89 R102 T104 A105 G131 A132 N133 R138 G139 K141 N142 A143 R144 E145 A146 K148 H149 F150

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0043232 intracellular non-membrane-bounded organelle
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8pvk, PDBe:8pvk, PDBj:8pvk
• PDBsum: 8pvk
• PubMed: 37921038
• UniProt: G0S9B5