Structure of PDB 6ip6 Chain 1E Binding Site BS01

Receptor Information

>6ip6 Chain 1E (length=402) Species: 9606 (Homo sapiens)

SHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKA
GMTHIVREVDRPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRT
FKTVFAEHISDECKRRFYKNWHKSKKKAFTKYCKKWQDEDGKKQLEKDFS
SMKKYCQVIRVIAHTQMRLLPLRQKKAHLMEIQVNGGTVAEKLDWARERL
EQQVPVNQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKLPRKTHRGLRKV
ACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIKN
NASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSL
LVQTKRRALEKIDLKFIDTTSKFGHGRFQTMEEKKAFMGPLKKDRIAKEE
GA

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): S2 H3 R4 K5 S7 R10 H11 S13 L14 F16 R19 K20 R21 H25 R26 K28 K30 S31 M53 H55 R62 G64 S65 A75 Y92 T95 R97 L99 R100 T101 F102 T104 R116 Y119 K120 H123 K124 S125 K126 K128 F130 T131 K132 K155 Y156 R161 R174 Q175 K176 K177 E182 T223 K224 G225 K226 G227 Y228 G230 K238 R242 K243 T244 H245 R246 G247 L248 R249 K250 A252 C253 I254 G255 A256 W257 H258 P259 A260 R261 V262 S265 R268 A269 Q271 Y274 H276 R277 T278 I280 K282 G318 V321 H322 G324 K334 G335 C336 V337 K342 R343 L352 R358 S372 K373 F374 G375 H376 R378 M382 K385 M389 P391 L392 K393 K394
• Binding residue (residue number reindexed from 1): S1 H2 R3 K4 S6 R9 H10 S12 L13 F15 R18 K19 R20 H24 R25 K27 K29 S30 M52 H54 R61 G63 S64 A74 Y91 T94 R96 L98 R99 T100 F101 T103 R115 Y118 K119 H122 K123 S124 K125 K127 F129 T130 K131 K154 Y155 R160 R173 Q174 K175 K176 E181 T222 K223 G224 K225 G226 Y227 G229 K237 R241 K242 T243 H244 R245 G246 L247 R248 K249 A251 C252 I253 G254 A255 W256 H257 P258 A259 R260 V261 S264 R267 A268 Q270 Y273 H275 R276 T277 I279 K281 G317 V320 H321 G323 K333 G334 C335 V336 K341 R342 L351 R357 S371 K372 F373 G374 H375 R377 M381 K384 M388 P390 L391 K392 K393

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0071353 cellular response to interleukin-4

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0032991 protein-containing complex
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6ip6, PDBe:6ip6, PDBj:6ip6
• PDBsum: 6ip6
• PubMed: 31080011
• UniProt: P39023|RL3_HUMAN Large ribosomal subunit protein uL3 (Gene Name=RPL3)