Structure of PDB 7qvp Chain Lf Binding Site BS01

Receptor Information

>7qvp Chain Lf (length=109) Species: 9606 (Homo sapiens)

SGRLWSKAIFAGYKRGLRNQREHTALLKIEGVYARDETEFYLGKRCAYVY
KAKNNTVTPGGKPNKTRVIWGKVTRAHGNSGMVRAKFRSNLPAKAIGHRI
RVMLYPSRI

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): S2 G3 R4 W6 K8 K15 R16 L18 R19 Q21 R22 E23 H24 Y34 R36 Y51 K52 K54 N55 N56 T57 T59 P60 T67 R68 V69 W71 K73 R76 H78 G79 N80 S81 R85 K87 N91 P93 A94 R100 R102 R109
• Binding residue (residue number reindexed from 1): S1 G2 R3 W5 K7 K14 R15 L17 R18 Q20 R21 E22 H23 Y33 R35 Y50 K51 K53 N54 N55 T56 T58 P59 T66 R67 V68 W70 K72 R75 H77 G78 N79 S80 R84 K86 N90 P92 A93 R99 R101 R108

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0042273 ribosomal large subunit biogenesis

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:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7qvp, PDBe:7qvp, PDBj:7qvp
• PDBsum: 7qvp
• PubMed: 36302773
• UniProt: P18077|RL35A_HUMAN Large ribosomal subunit protein eL33 (Gene Name=RPL35A)