Structure of PDB 7qvp Chain Lb Binding Site BS01

Receptor Information

>7qvp Chain Lb (length=75) Species: 9606 (Homo sapiens)

AKSKNHTTHNQSRKWHRNGIKKPRSQRYESLKGVDPKFLRNMRFAKKHNK
KGLKKMQANNAKAMSARAEAIKALV

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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<<<<...<<..<<<.<<.<<<<......<<<<<<<<..>>>>>>>>....
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..........<<<<<<.<<<<<<<....>>>>>>>.<<<<<<.<<<<.<<
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>>....>>>>>>......>>.>>>>>...>>>>>...>>>>>>>>..<<<
<........>>>><<<<<<....<<<<<<<<<<<<<..<<<...<<<<..
......>>>>.....>>>...<<....>>...<<<<<<<......>>>>>
>>..<<<<<...<<<..<<<....[[.((((>>>..>>>....>>>>>.<
<<<<<<<<.<<<<......>>>>>>>>>>>.>>....>>>>>>>>>>>>>
..<<.<..<<<<<<<.....<<<<<<<<<..<<<....<<<<<<<....>
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>>>>>>...<<.......>>......>>>>>>...>..>.>>..<<<<<<
....<.<<<....>>>.><<.<<<<<<<...................<<<
.<<<<<<<<<...<<<....<<<..<.<<<.....<<<........>>>.
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>>>>>>>>....>>>>>>>>>>>>..>>..<<<<.<<<<<.....>>>>>
.>>>>....<<<......>>>...<<<<<<<...<<<(((.......<<<
<<.....<<..........<<<.<<<<<<<<<<.......<<<<..<<..
..>>.....>>>>...>>>>>>>>>>>>>..........))).>>...>>
>>>..>>>...>>>>>>><<<<<<.<<<..........)))).]].....
.............................>>>>>>>>>....>>>>>>.<
<<<<<<<<<.<<......<<<<.<<<<....>>>>>>>>...>>>>>>>>
>>.>>.....>>>>>><<.....<<.....<<<<<<.......>>>>>>.
<<<.....<<<<<.<<...<<<<<<...<<.....>>.>>>>>>....((
<<<<<<...<<....<<<....>>>..........<<.<<<<<.......
....>>>>>>>......>>....>>>..<<<<<........>>>>>))<<
<<....<<<<<..<<<<<<<<....>>>>>>>>..<<<....>>>...<.
.<<<<<<<...<<<<<<<<<<<<.<<<<<<<<<<..{{{..>>>>>>...
.<<<<<.<<<<.<<<<.....<<<.....>>>.....>>>>>>>>..>>>
>>.....<<<<<<<.......>>>>>>>>>>>...>>>>>>>>>>>>...
......>>>>>>>..>..........>>.>>>.>>>>.>>>..>>.....
<<......>>>>>>>.<<<<.....>>>>..>>>....<<<<.....<<<
<<<<.<<.........<.....<<<<<....<<..>>.....>>>>><<.
<<<<<<<<<<<.......................>>>>>..>>>>>>.>>
............<<<<<<<<<..<<<.........>>>..<<<<<<<...
.<<<<.....>>>>......>>>>>>>...<<..<<<..<<<<<<....<
<<...<.<<<<....>>>>.>...>>>.>>>>..>>>>><<<<<<.....
..>>>>>>........<...........<<<<<.......>>>>>.....
>.....>>....>>.>>>>>>>..>..>>.>>>>>>>..>>>>>>....>
>....<<<<<........>>>>>....[[[[[..{{{.{{......[[[[
.{{[[[[..<<<<<.<<<<<<<<<.<<<<<<<<......>>>>>>>>...
<<<<<.....<<<<........<........>..................
.<<<<<<<<<<.......>>>>>>>>>>..>>>>..>>>>>....>>>>>
>>>>..>>>>>...<<<.....>>>..<<<<<<...........>>>>>>
..<<...<<<<<<<...<<<<<<.......>>>>>>.....<<.[.(((>
>....>>>>>>>...<<<..<<<<.......>>>>..>>><<<<....>>
>>>>)))]......((((((..(((..>>>>>>.))))))))).......
...]]]]..}}]]]].......<<.<.<.<<<<<<...<<.......>>.
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...>>>>>...>.>.<<<.........>>>.....>>>>>..>...>>>.
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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): K3 S4 K5 N6 H7 T8 T9 H10 N11 S13 R14 K15 H17 R18 N19 K22 S26 Q27 R28 Y29 L32 D36 K38 R41 N42 R44 F45 A46 K47 K48 H49 N50 K52 G53 K56 M57 N60 N61
• Binding residue (residue number reindexed from 1): K2 S3 K4 N5 H6 T7 T8 H9 N10 S12 R13 K14 H16 R17 N18 K21 S25 Q26 R27 Y28 L31 D35 K37 R40 N41 R43 F44 A45 K46 K47 H48 N49 K51 G52 K55 M56 N59 N60

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0008201 heparin binding
• GO:0045296 cadherin binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0007566 embryo implantation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7qvp, PDBe:7qvp, PDBj:7qvp
• PDBsum: 7qvp
• PubMed: 36302773
• UniProt: P47914|RL29_HUMAN Large ribosomal subunit protein eL29 (Gene Name=RPL29)