Structure of PDB 6ip8 Chain 2F Binding Site BS01

Receptor Information

>6ip8 Chain 2F (length=210) Species: 9606 (Homo sapiens)

APSRNGMVLKPHFHKDWQRRVATWFNQPARKIRRRKARQAKARRIAPRPA
SGPIRPIVRCPTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPR
RRNKSTESLQANVQRLKEYRSKLILFPRKPSAPKKGDSSAEELKLATQLT
GPVMPVRNVYKKEKARVITEEEKNFKAFASLRMARANARLFGIRAKRAKE
AAEQDVEKKK

Ligand information

>6ip8 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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>>>>>>>>>>......>>>.>>>.>>>>>...<<<<<<<.<<<<<<<<<<
.<<<<...<<..<<<....<<<<......<<<<<<<....>>>>>>>...
....>>>>...>>>........>>>>>>...>>>>>>>>>>.........
...........<<<<<<.<<<<<<<............>>>>>>>.<<<<<
<.<<<<.<<<<<<<<<<<.<<<<<.<<<<..<...........>...>>>
>.>>>>>.>.>>>>>>>.>>>...>>>>..>>>>.>>..<<<<<<<<<<.
....>>>>>>>>.>>....>>>>>>......>>.>>>>>...>>>>>...
>>>>>>>>..<<<<........>>>><<<<<<....<<<<<<<<<<<<<.
.<<<...<<<<........>>>>.....>>>...<<....>>...<<<<<
<<......>>>>>>>..<<<<<...<<<..<<<..[[...((((>>>..>
>>....>>>>>.<<<<<<<<<.<<<<......>>>>>>>>>>>.>>....
>>>>>>>>>>>>>..<<.<..<<<<<<<.....<<<<<<<<<..<<<...
.<<<<<<<....>>>>>>>.....>>>...<<<..<<.<<........>>
>>.>>>....>>>>>>>>>...<<.......>>......>>>>>>...>.
.>.>>..<<<<<<....<.<<<....>>>.><<<<<<<<<<.........
.............<<<.<<<<<<<<<...<<<....<<<..<.<<<....
.<.............>...>>>.>..>>>..>.>>...>>>>>>>...<<
<<<<<<<.<......>>>>>>>>>>....>>>>>>>>>>>>.>>>..<<<
<.<<<<<.....>>>>>.>>>>....<<<......>>>...<<<<<<<..
.<<<(((.......<<<<<.....<<..........<<<.<<<<<<<<<<
..........<..<<.....................>>............
...........>......>>>>>>>>>>>>>..........))).>>...
>>>>>..>>>...>>>>>>><<<<<<.<<<..........))))...]].
..<.....>..................>>>>>>>>>....>>>>>>.<<<
<<<<<<..<<......<<<<.<<<<....>>>>>>>>...>>.>>>>>>>
.>>.....>>>>>><<<....<<.....<<<<<<.......>>>>>>.<<
<.....<<<<<.<<...<<<<<<...<<.....>>.>>>>>>....((<<
<<<<...<<....<<<....>>>..........<<.<<<.<...<...>.
..>.>>>>>......>>....>>>..<<<<<........>>>>>))<<<<
....<<<<....<<<<<<.....>.>>>>>...<<<....>>>...<..<
<<<<<<...<<<<<<<<<<<<<<<<<<<<<<<..{{{..>>>>>>....<
<<<<.<<<<.<<<<.....<<<.....>>>.....>>>>>>>>..>>>>>
.....<<<<<<<.......>>>>>>>>>>>.>.>>>>>>>>>>>>.....
....>>>>>>>..>..........>..>>>.>>>>.>>>..>>.....<<
......>>>>>>>.<<<<.....>>>>..>>>....<<<<.....<<<<<
<<.<<...............<<<<<....<<..>>.....>>>>><<.<<
<<<<<<<<<......<.....>...........>>>>>..>>>>>>.>>.
...........<<<<<<<<<..<<<.........>>>..<<<<<<<....
<<<<.....>>>>......>>>>>>>...<<..<<<..<<<<<<.....<
<.....<<<<....>>>>.....>>..>>>>..>>>>><<<.........
...>>>.........<...........<<<<<.......>>>>>.....>
.....>>....>>.>>>>>>>.....>>.>>>>>>>..>>>>>>...>>>
....<<<<<........>>>>>.....[[[[..{{{.{{......[[[[.
{.[[[[..<<<<<.<<<<<<<<<.<<<<<<<<.<..........>.>>>>
>>>>...<<<<<.....<<<<.........<.....>.............
........<<<<<<<<<<<.....>>>>>>>>>>>..>>>>..>>>>>..
..>>>>>>>>>..>>>>>...<<<.....>>>..<<<<<<..........
.>>>>>>..<<...<<<<<<<...<<<<<<.......>>>>>>.....<<
.[.(((>>....>>>>>>>...<<<.<<<<<.......>>>>.>>>>.<<
<....>>>.>>)))]......((((((..(((..>>>>>>.)))))))))
..........]]]]...}]]]].......<<.<.<.<<<<<<...<<...
....>>...>>>>>>...>>.>.>.......<<<<<.<<<<<<..<.<.<
<<<<......>>>>>...>.>.<<<.........>>>.....>>>>>..>
...>>>.>>....<<<<<<<....>>>.>>>>....}}..}}}.]]]]..
....<<<<<<.<..<<<..<.<<<<<.................>>>>>.>
<<<<....<<<<....<<.<<<<<<.}}}..>>>>..>>.>>...>>>>.
..>>>><.<<....<<<<<...........>>>>>.....>>>.>>>...
>.>>>>>>.....<<<<<<<.<...<<<.....<<.........<<<<<.
.<<<<..>>>>.>>>>>........>>..........<<....<<<<.<<
<<<<<......>>>>>>>>>>>....>>....................>>
>...>.>>>>>>><<<<<.<.............>....<<.<<<<<<<.<
<.....<<<<....<<<<<......>>>>>...>>>>....>>....>>>
>.>>>.>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6ip8 HCV IRES Captures an Actively Translating 80S Ribosome.
• Resolution: 3.9 Å
• Binding residue (original residue number in PDB): A2 R5 M8 L10 K11 H13 H15 K16 W18 Q19 R21 Q28 R31 K32 R35 R36 R39 R44 R56 V59 R60 C61 P62 Y66 H67 R71 R74 L78 K88 K89 R92 D99 R101 R102 R103 S106 K135 R158 K163 K165 A166 R183 M184 R186 R190 L191 I194 R195 R198
• Binding residue (residue number reindexed from 1): A1 R4 M7 L9 K10 H12 H14 K15 W17 Q18 R20 Q27 R30 K31 R34 R35 R38 R43 R55 V58 R59 C60 P61 Y65 H66 R70 R73 L77 K87 K88 R91 D98 R100 R101 R102 S105 K134 R157 K162 K164 A165 R182 M183 R185 R189 L190 I193 R194 R197

Gene Ontology

Molecular Function

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

Biological Process

• GO:0001824 blastocyst development
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0060348 bone development

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6ip8, PDBe:6ip8, PDBj:6ip8
• PDBsum: 6ip8
• PubMed: 31080011
• UniProt: P26373|RL13_HUMAN Large ribosomal subunit protein eL13 (Gene Name=RPL13)