Structure of PDB 6ip6 Chain 2g Binding Site BS01

Receptor Information

>6ip6 Chain 2g (length=52) Species: 9606 (Homo sapiens)

IIEPSLRQLAQKYNCDKMICRKCYARLHPRAVNCRKKKCGHTNNLRPKKK
VK

Ligand information

>6ip6 Chain 1A (length=3667)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgg
cccggcggaucuuucccgcgcgggggaccgucccccgaccggcgaccggc
cgccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccggg
acggcugggaaggcccggcggggaagguggcucgggggcccccgaguguu
acagcccccccggcagcagcacucgccgaaucccggggccgagggagcga
gacccgucgccgcgcucuccccccucccggcgcgccggggggggccgggc
caccccucccacggcgcgaccgcucggggcggacuguccccagugcgccc
cgggcgggucgcgccgucgggcccgggggaggccacgcgcgcgucccccg
aagagggggacggcggagcgagcgcacggggucggcggcgacgucggcua
cccacccgacccgucuugaaacacggaccaaggagucuaacacgugcgcg
agucgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggccg
gcgcgcucgccggccgaggugggaucccgaggccucuccaguccgccgag
ggcgcaccaccggcccgucucgcccgccgcgccggggagguggagcacga
gcgcacguguuaggacccgaaagauggugaacuaugccugggcagggcga
agccagaggaaacucugguggagguccguagcgguccugacgugcaaauc
ggucguccgaccuggguauaggggcgaaagacuaaucgaaccaucuagua
gcugguucccuccgaaguuucccucaggauagcuggcgcucucgcagacc
cgacgcccgccacgcaguuuuauccgguaaagcgaaugauuagaggucuu
ggggccgaaacgaucucaaccuauucucaaacuuuaaauggguaagaagc
ccggcucgcuggcguggagccgggcguggaaugcgagugccuagugggcc
acuuuugguaagcagaacuggcgcugcgggaugaaccgaacgccggguua
aggcgcccgaugccgacgcucaucagaccccagaaaagguguugguugau
auagacagcaggacgguggccauggaagucggaauccgcuaaggagugug
uaacaacucaccugccgaaucaacuagcccugaaaauggauggcgcugga
gcgucgggcccauacccggccgucgccggcagucgagaguggacgggagc
ggcggcccggagccccgcggacgcuacgccgcgacgaguaggagggccgc
ugcggugagccuugaagccuagggcgcgggcccggguggagccgccgcag
gugcagaucuuggugguaguagcaaauauucaaacgagaacuuugaaggc
cgaaguggagaaggguuccaugugaacagcaguugaacaugggucagucg
guccugagagaugggcgagcgccguuccgaagggacgggcgauggccucc
guugcccucggccgaucgaaagggagucggguucagauccccgaauccgg
aguggcggagaugggcgccgcgaggcguccagugcgguaacgcgaccgau
cccggagaagccggcgggagccccggggagaguucucuuuucuuugugaa
gggcagggcgcccuggaauggguucgccccgagagaggggcccgugccuu
ggaaagcgucgcgguuccggcggcguccggugagcucucgcuggcccuug
aaaauccgggggagaggguguaaaucucgcgccgggccguacccauaucc
gcagcaggucuccaaggugaacagccucuggcauguuggaacaauguagg
uaagggaagucggcaagccggauccguaacuucgggauaaggauuggcuc
uaagggcugggucggucgucggccggcgccuagcagccgacuuagaacug
gugcggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaag
gcccgcggcggguguugacgcgaugugauuucugcccagugcucugaaug
ucaaagugaagaaauucaaugaagcgcggguaaacggcgggaguaacuau
gacucucuuaagguagccaaaugccucgucaucuaauuagugacgcgcau
gaauggaugaacgagauucccacugucccuaccuacuauccagcgaaacc
acagccaagggaacgggcuuggcggaaucagcggggaaagaagacccugu
ugagcuugacucuagucuggcacggugaagagacaugagugaucguuuuu
ucacugacccggugaggcgggggggcgagccccgaggggcucucgcuucu
ggcgccaagcgcccggccgcgcgccggccgggcgcgacccgcuccgggga
cagugccagguggggaguuugacuggggcgguacaccugucaaacgguaa
cgcagguguccuaaggcgagcucagggaggacagaaaccucccguggagc
agaagggcaaaagcucgcuugaucuugauuuucaguacgaauacagaccg
ugaaagcggggccucacgauccuucugaccuuuuggguuuuaagcaggag
gugucagaaaaguuaccacagggauaacuggcuuguggcggccaagcguu
cauagcgacgucgcuuuuugauccuucgaugucggcucuuccuaucauug
ugaagcagaauucaccaagcguuggauuguucacccacuaauagggaacg
ugagcuggguuuagaccgucgugagacagguuaguuuuacccuacugaug
auguguuguugccaugguaauccugcucaguacgagaggaaccgcagguu
cagacauuugguguaugugcuuggcugaggagccaauggggcgaagcuac
caucugugggauuaugacugaacgccucuaagucagaaucccgcccaggc
ggaacgauacggcagcgccgcggagccucgguuggccucggauagccggu
cccccgcgggguccggugcggagugcccuucguccugggaaacggggcgc
ggccggagaggcggccgcccccucgcccgucacgcaccgcacguucgugg
ggaaccuggcgcuaaaccauucguagacgaccugcuucugggucgggguu
ucguacguagcagagcagcucccucgcugcgaucuauugaaagucagccc
ucgacacaaggguuugu

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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: 6ip6 HCV IRES Captures an Actively Translating 80S Ribosome.
• Resolution: 4.5 Å
• Binding residue (original residue number in PDB): R97 Y100 A101 R102 H104 R106 N109 R111 K112 K114 G116 H117 R122 K124 K125
• Binding residue (residue number reindexed from 1): R21 Y24 A25 R26 H28 R30 N33 R35 K36 K38 G40 H41 R46 K48 K49

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0031386 protein tag activity
• GO:0031625 ubiquitin protein ligase binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0016567 protein ubiquitination
• GO:0019941 modification-dependent protein catabolic process
• GO:0036211 protein modification process

Cellular Component

• GO:0005615 extracellular space
• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005737 cytoplasm
• GO:0005741 mitochondrial outer membrane
• GO:0005765 lysosomal membrane
• GO:0005783 endoplasmic reticulum
• GO:0005789 endoplasmic reticulum membrane
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005886 plasma membrane
• GO:0010008 endosome membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0030666 endocytic vesicle membrane
• GO:0031982 vesicle
• GO:0045202 synapse
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6ip6, PDBe:6ip6, PDBj:6ip6
• PDBsum: 6ip6
• PubMed: 31080011
• UniProt: P62987|RL40_HUMAN Ubiquitin-ribosomal protein eL40 fusion protein (Gene Name=UBA52)