Structure of PDB 7qvp Chain LO Binding Site BS01

Receptor Information

>7qvp Chain LO (length=200) Species: 9606 (Homo sapiens)

VQVLVLDGRGHLLGRLAAIVAKQVLLGRKVVVVRCEGINISGNFYRNKLK
YLAFLRKRMNTNPSRGPYHFRAPSRIFWRTVRGMLPHKTKRGQAALDRLK
VFDGIPPPYDKKKRMVVPAALKVVRLKPTRKFAYLGRLAHEVGWKYQAVT
ATLEEKRKEKAKIHYRKKKQLMRLRKQAEKNVEKKIDKYTEVLKTHGLLV

Ligand information

>7qvp Chain L5 (length=3611)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcgguccggccgugucggcggc
ccggcggaucuuucccgcgcgggggaccgucccccgaccggcgaccggcc
gccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccggga
cggcugggaaggcccggcggggaagguggcucgggggcccccgaguguua
cagcccccccggcagcagcacucgccgaaucccggggccgagggagcgag
acccgucgccgcgcucuccccccucccggggggggccgggccaccccucc
cacggcgcgaccgcucggggcggacuguccccagugcgccccgggcgggu
cgcgccgucgggcccgggggggccacgcgcgcgucccccgagggggacgg
cggagcgagcgcacggggucggcggcgacgucggcuacccacccgacccg
ucuugaaacacggaccaaggagucuaacacgugcgcgagucgggggcucg
cacgaaagccgccguggcgcaaugaaggugaaggccggcgcgcucgccgg
ccgaggugggaucccgaggccucuccaguccgccgagggcgcaccaccgg
cccgucucgcccgccgcgccggggagguggagcacgagcgcacguguuag
gacccgaaagauggugaacuaugccugggcagggcgaagccagaggaaac
ucugguggagguccguagcgguccugacgugcaaaucggucguccgaccu
ggguauaggggcgaaagacuaaucgaaccaucuaguagcugguucccucc
gaaguuucccucaggauagcuggcgcucucgcagacccgaccgccacgca
guuuuauccgguaaagcgaaugauuagaggucuuggggccgaaagaucuc
aaccuauucucaaacuuuaaauggguaagaagcccggcucgcuggcgugg
agccgggcguggaaugcgagugccuagugggccacuuuugguaagcagaa
cuggcgcugcgggaugaaccgaacgccggguuaaggcgcccgaugccgac
gcucaucagaccccagaaaagguguugguugauauagacagcaggacggu
ggcgcuaaccugccgaaucaacuagcccugaaaauggauggcgcuggagc
gucgggcccauacccggccgucgccggcagucgagaguggacgggagcgg
cggcgcgcccggagccccgcggacgcuacgccgcgacgaguaggagggcc
gcugcggugagccuugaagccuagggcgcgggcccggguggagccgccgc
aggugcagaucuuggugguaguagcaaauauucaaacgagaacuuugaag
gccgaaguggagaaggguuccaugugaacagcaguugaacaugggucagu
cgguccugagagaugggcgagcgccguuccgaagggacgggcgauggccu
ccguugcccucggccgaucgaaagggagucggguucagauccccgaaucc
ggaguggcggagaugggcgccgcgaggcguccagugcgguaacgcgaccg
aucccggagaagccggcgggagccccggggagaguucucuuuucuuugug
aagggcagggcgcccuggaauggguucgccccgagagaggggcccgugcc
uuggaaagcgucgcgguuccggcggcguccggugagcucucgcuggcccu
ugaaaauccgggggagaggguguaaaucucgcgccgggccguacccauau
ccgcagcaggucuccaaggugaacagccucuggcauguuggaacaaugua
gguaagggaagucggcaagccggauccguaacuucgggauaaggauuggc
ucuaagggcugggucggucgcggccggcgccuagcagccgacuuagaacu
ggugcggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaa
ggcccgcggcggguguugacgcgaugugauuucugcccagugcucugaau
gucaaagugaagaaauucaaugaagcgcggguaaacggcgggaguaacua
ugacucucuuaagguagccaaaugccucgucaucuaauuagugacgcgca
ugaauggaugaacgagauucccacugucccuaccuacuauccagcgaaac
cacagccaagggaacgggcuuggcggaaucagcggggaaagaagacccug
uugagcuugacucuagucuggcacggugaagagacacguuuuuucacuga
cccggugaggcgggggggcgagccccgaggggcucucgcuucuggcgcca
agcgcccggccgcgcgccggccgggcgcgacccgcuccggggacagugcc
agguggggaguuugacuggggcgguacaccugucaaacgguaacgcaggu
guccuaaggcgagcucagggaggacagaaaccucccguggagcagaaggg
caaaagcucgcuugaucuugauuuucaguacgaauacagaccgugaaagc
ggggccucacgauccuucugaccuuuuggguuuuaagcaggaggugucag
aaaaguuaccacagggauaacuggcuuguggcggccaagcguucauagcg
acgucgcuuuuugauccuucgaugucggcucuuccuaucauugugaagca
gaauucaccaagcguuggauuguucacccacuaauagggaacgugagcug
gguuuagaccgucgugagacagguuaguuuuacccuacugaugauguguu
guugccaugguaauccugcucaguacgagaggaaccgcagguucagacau
uugguguaugugcuuggcugaggagccaauggggcgaagcuaccaucugu
gggauuaugacugaacgccucuaagucagaaucccgcccaggcggaacga
uacggcagcgccgcggagccucgguuggccucggauagccggucccccgc
cgggguccggugcggagugcccuucguccugggaaacggggcgcggccgg
agaggcggccgcccccucgcccgucacgcaccgcacguucguggggaacc
uggcgcuaaaccauucguagacgaccugcuucugggucgggguuucguac
guagcagagcagcucccucgcugcgaucuauugaaagucagcccucgaca
caaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7qvp A distinct mammalian disome collision interface harbors K63-linked polyubiquitination of uS10 to trigger hRQT-mediated subunit dissociation.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): R12 G17 R18 K25 L28 R37 S44 N46 Y48 R49 R59 K60 R61 M62 N63 N65 P66 R68 P70 Y71 H72 F73 R74 R82 T83 R85 G86 M87 P89 H90 K91 K93 R94 F105 D106 G107 I108 P110 D113 K114 K115 K116 R117 M118 V126 V127 R128 L129 K130 R133 K134 E144 V145 K148 Y149 L156 E157 K159 R160 K161 K163 H167 Y168 R169 K171 K172 M175 R176 K179 K188 V203
• Binding residue (residue number reindexed from 1): R9 G14 R15 K22 L25 R34 S41 N43 Y45 R46 R56 K57 R58 M59 N60 N62 P63 R65 P67 Y68 H69 F70 R71 R79 T80 R82 G83 M84 P86 H87 K88 K90 R91 F102 D103 G104 I105 P107 D110 K111 K112 K113 R114 M115 V123 V124 R125 L126 K127 R130 K131 E141 V142 K145 Y146 L153 E154 K156 R157 K158 K160 H164 Y165 R166 K168 K169 M172 R173 K176 K185 V200

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0006417 regulation of translation
• GO:0017148 negative regulation of translation
• GO:0032496 response to lipopolysaccharide
• GO:0042592 homeostatic process
• GO:0048246 macrophage chemotaxis
• GO:0060425 lung morphogenesis
• GO:0071346 cellular response to type II interferon
• GO:1901194 negative regulation of formation of translation preinitiation complex

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0015934 large ribosomal subunit
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:0097452 GAIT complex
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7qvp, PDBe:7qvp, PDBj:7qvp
• PDBsum: 7qvp
• PubMed: 36302773
• UniProt: P40429|RL13A_HUMAN Large ribosomal subunit protein uL13 (Gene Name=RPL13A)