Structure of PDB 6ip6 Chain 2H Binding Site BS01

Receptor Information

>6ip6 Chain 2H (length=203) Species: 9606 (Homo sapiens)

GAYKYIQELWRKKQSDVMRFLLRVRCWQYRQLSALHRAPRPTRPDKARRL
GYKAKQGYVIYRIRVRRGGRKRPVPKGATYGKPVHHGVNQLKFARSLQSV
AEERAGRHCGALRVLNSYWVGEDSTYKFFEVILIDPFHKAIRRNPDTQWI
TKPVHKHREMRGLTSAGRKSRGLGKGHKFHHTIGGSRRAAWRRRNTLQLH
RYR

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

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): Y4 Q8 R12 K14 Q15 R24 S34 A35 H37 P40 R41 R44 K47 R49 R50 K54 A55 R65 R67 R68 G70 R71 K72 P76 K77 Y81 G82 K83 P84 V85 H86 V89 N90 Q91 K93 F94 A95 R96 S97 L98 E104 R105 R108 A112 S125 F138 W150 M161 R162 L164 S166 R169 K170 S171 R172 K176 H178 K179 H181 H182 I184 G185 S187 R189 W192 R193 R194 R195 H201 R202 R204
• Binding residue (residue number reindexed from 1): Y3 Q7 R11 K13 Q14 R23 S33 A34 H36 P39 R40 R43 K46 R48 R49 K53 A54 R64 R66 R67 G69 R70 K71 P75 K76 Y80 G81 K82 P83 V84 H85 V88 N89 Q90 K92 F93 A94 R95 S96 L97 E103 R104 R107 A111 S124 F137 W149 M160 R161 L163 S165 R168 K169 S170 R171 K175 H177 K178 H180 H181 I183 G184 S186 R188 W191 R192 R193 R194 H200 R201 R203

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0045296 cadherin binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0045471 response to ethanol

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0031672 A band
• GO:0044391 ribosomal subunit
• GO:0045202 synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6ip6, PDBe:6ip6, PDBj:6ip6
• PDBsum: 6ip6
• PubMed: 31080011
• UniProt: P61313|RL15_HUMAN Large ribosomal subunit protein eL15 (Gene Name=RPL15)