Structure of PDB 6p5n Chain AF Binding Site BS01

Receptor Information

>6p5n Chain AF (length=225) Species: 9986 (Oryctolagus cuniculus)

NFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKEYRQMYRTEIRMAR
MARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGTFV
KLNKASINMLRIVEPYIAWGYPNLKSVNELIYKRGYGKINKKRIALTDNT
LIARSLGKYNIICMEDLIHEIYTVGKHFKEANNFLWPFKLSSPRGGMKKK
TTHFVEGGDAGNREDQINRLIRRMN

Ligand information

>6p5n Chain 5 (length=3594)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggaaaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggaaau
guggcguacggaagacccacuccccggcgccggggggcccaaguccuucu
gaucgaggcccagcccguggacggugugaggccgguagcggcccccggcg
cgccgggcccgggucuucccggagucggguugcuugggaaugcagcccaa
agcgggugguaaacuccaucuaaggcuaaauaccggcacgagaccgauag
ucaacaaguaccguaagggaaaguugaaaagaacuuugaagagagaguuc
aagagggcgugaaaccguuaagagguaaacgggugggguccgcgcagucc
gcccggaggauucaacccggcggcggguccggccgugccggcggggcgga
ucucccgcucccgucggcgggggaccgccccccggccggcgaccggccgc
cgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccgggacg
gcugggaaggcccggcggggaagguggcccgggggccccggguguuacag
cccacccggcagcagcagcucgccgaaucccggggccgagggagcgagac
cugugucgccgcgcucuccccccugggggggccgggccaccccucccacg
gcgcgaccgcuggggcggacuguccagugcgccccgggcgggucgcgccg
ucgggcccggggggccacgcgucccccgcgagcgcacggggucggcggcg
augucggcuacccacccgacccgucuugaaacacggaccaaggagucuaa
cacgugcgcgagucgggggcuacgaaagccgccguggcgcaaugaaggug
aaggccggcgccgccggccgaggugggaucccgaggccuuccaguccgcc
gagggcgcaccaccggcccgucucgcccgccgcgccggggagguggagca
cgagcgcacguguuaggacccgaaagauggugaacuaugccugggcaggg
cgaagccagaggaaacucugguggagguccguagcgguccugacgugcga
aucggucguccgaccuggguauaggggcgaaagacuaaucgaaccaucua
guagcugguucccuccaaaguuucccucaggauagcuggcgcucuccgca
guuuuauccgguaaagcgaaugauuagaggucuuggggccgaaacgaucu
caaccuauucucaaacuuuaaauggguaagaagcccggcucgcuggugug
gagccgggcguggaaugcgagugccuagugggccacuuuugguaagcaga
acuggcgcugcgggaugaaccgaacgccggguuaaggcgcccgaugccga
cgcucaucagaccccagaaaagguguugguugauauagacagcaggaugg
uggccauggaagucggaauccgcuaaggaguguguaacaacucaccugcc
gaaucaacuagcccugaaaauggauggcgcuggagcgucgggcccauacc
cggccgucgcuggcagucggcagagcgagaaagagaguggcgcggacgcu
acgccgcgacgaguaggagggccgcugcggugagccuugaagccuagggc
gcgggcccggguggagccgccgcaggugcagaucuuggugguaguagcaa
auauucaaacgagaacuuugaaggccgaaguggagaaggguuccauguga
acagcaguugaacaugggucagucgguccugagagaugggcgagcgccgu
uccgaagggacgggcgauggccuccguugcccucagccgaucgaaaggga
gucggguucagauccccgaauccggaguggcggagaugggcgccgcgagg
cguccagugcgguaacgcgaccgaucccggagaagccggcgggagccccg
gggagaguucucuuuucuuugugaagggcagggcgcccuggaauggguuc
gccccgagagaggggcccgugccuuggaaagcgucgcgguuccggcggcg
uccggugagcucucgcuggcccuugaaaauccgggggagaggguguaaau
cucgcgccgggccguacccauauccgcagcaggucuccaaggugaacagc
cucuggcauguuggaacaauguagguaagggaagucggcaagccggaucc
guaacuucgggauaaggauuggcucuaagggcuggcagccgacuuagaac
uggugcggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcga
aggcccgcggcggguguugacgcgaugugauuucugcccagugcucugaa
ugucaaagugaagaaauucaaugaagcgcggguaaacggcgggaguaacu
augacucucuuaagguagccaaaugccucgucaucuaauuagugacgcgc
augaauggaugaacgagauucccacugucccuaccuacuauccagcgaaa
ccacagccaagggaacgggcuuggcggaaucagcggggaaagaagacccu
guugagcuugacucuagucuggcacggugaagagacaugagagguguaga
auaagugggaggcccgggccgccggugaaauaccacuacucugaucguuu
uuucacugacccggugaggcgggggggcgagccgggcucucgcuucuggc
gccaagcgcccggccggccgggcgcgacccgcuccggggacagugccagg
uggggaguuugacuggggcgguacaccugucaaacgguaacgcagguguc
cuaaggcgagcucagggaggacagaaaccucccguggagcagaagggcaa
aagcucgcuugaucuugauuuucaguacgaauacagaccgugaaagcggg
gccucacgauccuucugaccuuuuggguuuuaagcaggaggugucagaaa
aguuaccacagggauaacuggcuuguggcggccaagcguucauagcgacg
ucgcuuuuugauccuucgaugucggcucuuccuaucauugugaagcagaa
uucaccaagcguuggauuguucacccacuaauagggaacgugagcugggu
uuagaccgucgugagacagguuaguuuuacccuacugaugauguguuguu
gccaugguaauccugcucaguacgagaggaaccgcagguucagacauuug
guguaugugcuuggcugaggagccaauggggcgaagcuaccaucuguggg
auuaugacugaacgccucuaagucagaaucccgcccaggcggaacgauag
cgccggagccucgguuggccucggauagccggucccccgccgggguccgg
ugcggagagcccuucgucccgggaaacggggcggccggaaagggggccgc
ccucucgcccgucacgcaccgcacguucguggggaaccuggcgcuaaacc
auucguagacgaccugcuucugggucgggguuucguacguagcagagcag
cugcugcgaucuauugaaagucagcccucgacacaaggguuugu

.........................<<<<<<.....<......>......
>>>>>.>.........<<....>>..<<<<<<.....<<.....>>....
>>>>>>..<<<..<<<<<...<<<<<<<<<<.....>>>>>>.>>>>...
..>>>>>..<<<<<<<<<....<<<<<<<<..<<<<<<<<....<<<<..
....>>>>.....((......<<<.....))>>>...>.>>>>>>>...>
>>>>>>>...>>>>>>>>>.......<<<<<<<........>>>>>>>..
...<<<<<..((((((>>>>>..>>>........................
..........<<....>>...............<<<<....>>>>.....
.............................<<<<<<<<..<<<.<....<<
<<<<<<.<<<.....<<<<<<<<<....<<<<<<<.<<<<<.<<<<<<<.
<<<<<<<.<<.....>>>>>>>>>>>>>>>>>>>>>>>>>...>>>..>>
>>>>>>>......>>>.>>>.>>>>>...<<<<<<<.<<<<<<<<<<<<<
<<...<<..<<..<<..<<<......<<<<<<<..>.>>>>>>.......
>>>..>>.>>.........>>>>>>..>>>>>>>>>>>.....<<.....
<.>>......<<<<<<.<<<<<<..>>>>>>...<.<<..<<<.<<<<<<
<<<<<<<<<<<<<<<<<.<<<<..>>>>.>>>>>>.>>>.>>>>>>>>>>
>.>>>...>>>.>>>..............>>>>>>......>>.>>>>>.
...>>>>...>>>>>>>>..<<<<........>>>><<<<<<....<<<<
<<<<<<<<<..<<<...<<<.......>>>.....>>>...<<....>>.
..<<<<<<<...>>>>>>>..<<<<<...<<<..<<<....[[.[..>>>
..>>>....>>>>>.<<<<<<<<<.<<<<......>>>>>>>>>>>.>>.
...>>>>>>>>>>>>>..<<.<..<<<<<<<.....<<<<<<<<<..<<<
....<<<<<<<....>>>>>>>.....>>>...<<<..<<.<<.......
.>>>>.>>>....>>>>>>>>>...<<.......>>......>>>>>>..
.>..>.>>..<<<<<<....<.<<<....>>>.><<.<<<<<<<...<<<
.<<<<<<<<<...<<<....<<<..<.<<<<..<<<.<.........>.>
>>>>>>.>..>>>..>.>>...>>>>>>>...<<<<<<<<<.<......>
>>>>>>>>>....>>>>>>>>>>>>..>>..<<<<.<<<<<.....>>>>
>.>>>>....<<<......>>>...<<<<<<<...<<<(((.......<<
<<<.....<<..........<<<.<<<<<<<<<<..........<<.<<.
...<<.........>>....>>.........<<......>>...>>....
..>>>>>>>>>>>>>..........))).>>...>>>>>..>>>...>>>
>>>><<<<<<.<<<........>............].]]...........
..>>>>>>>>>....>>>>>>.<.<<<<<<<<.<<......<<<<.<<<<
....>>>>>>>>...>>>>>>>>>>..>.....>>>>>><<<....<<..
...<<<<<<.......>>>>>>.<<<.....<<<<<.<<...<<<<<<..
.<<.....>>.>>>>>>....(.<<<<<<...<<....<<<....>>>..
........<<.<<<<<.<<<...>>>.>>>>>>>......>>....>>>.
.<<<<<........>>>>>.)<<<<....<<<<<..<<<<<<<<....>>
>>>>>>..<<<....>>>...<..<<<<<<<...<<<<<<<<<<<<.<<<
<<<<<<<..[[[..>>>>>>....<<<<<.<<<<.<<<<.....<<<...
..>>>.....>>>>>>>>..>>>>>.....<<<<<<<.......>>>>>>
>>>>>...>>>>>>>>>>>>.........>>>>>>>..>..........>
>.>>>.>>>>.>>>..>>.....<<......>>>>>>>.<<<<.....>>
>>..>>>....<<<<.....<<<<<<<.<<.........<.....<<<<<
....<<..>>.....>>>>><<.<<<<<<<<<<<.>>>>>..>>>>>>.>
>............<<<<<<<<<..<<<.........>>>..<<<<<<<..
..<<<<.....>>>>......>>>>>>>...<<..<<<..<<<<<<....
<<<.....<<<<....>>>>.....>>>.>>>>..>>>>>.<<<<<....
...>>>>>.........<...........<<<<<.......>>>>>....
.>.....>>....>>.>>>>>>>..>..>>.>>>>>>>..>>>>>>...>
>>....<<<<<........>>>>>....<<<<<..<<<.<<......<<<
<.<<<<<<..<<<<<.<<<<<<<<<.<<<<<<<<<<<<.<<<<.......
...<<<.....<<<..>>>...............>>>.>>>>.>>.>>>>
>>>>>>...<<<<<.....<<<<...<....<<>>....>..........
.....<<<<<<<<<..>>>>>>>>>..>>>>..>>>>>....>>>>>>>>
>..>>>>>...<<<.....>>>..<<<<<<...........>>>>>>..<
<...<<<<<<<...<<<<<<.......>>>>>>.....<<.[.(((>>..
..>>>>>>>...<<<..<<<<.......>>>>..>>>.<<<....>>>.>
>)))].....<<<<<<<..<<<..)))))).>>>>>>>>>>.........
>>>>..>>>>>>.......<<.<.<.<<<<<<...<<.......>>...>
>>>>>...>>.>.>.......<<<<<.<<<<<<..<.<.<<<<<......
>>>>>...>.>.<<<.........>>>.....>>>>>..>...>>>.>>.
...<<<<<<<....>>>.>>>>....>>..>>>.>>>>>.....<<<<<<
.<..<<<..<.<<<<<.................>>>>>.><<<<....<<
<<....<<.<<<<<<<]]].>>>>>..>>.>>...>>>>...>>>><<<<
....<<<<<...........>>>>>....>>>>.>>>...>.>>>>>>.<
<<<<<<..<<<<....<<<........<<<<<.<.<<<<.>>>>>.>>>>
>.......>>>...<<<..<<<<....<<....<.............>..
..>>...>>>>..>>>..............>>>>..>.>>>>>>.<<<<<
.<.............>....<<.<<<<<<<.<<.....<<<<.<..<<<<
<.>>>>>..>>>>>....>>....>>>>.>>>.>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6p5n The Israeli acute paralysis virus IRES captures host ribosomes by mimicking a ribosomal state with hybrid tRNAs.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): F24 K28 I29 R31 L32 R33 K34 F36 R45 R46 K47 Y50 H57 K58 Y60 R61 Y64 R65 I68 R69 M70 R72 M73 R75 K76 R95 G96 I97 N98 G99 P102 K103 K106 L110 R112 I116 K126 A127 N130 M131 N145 L146 K147 N150 R156 K160 K164 R165 T172 A175 G179 I184 E187 K201 N205 K211 L212 S213 S214 P215 R216 G217 G218 M219 K221 K222 R241
• Binding residue (residue number reindexed from 1): F2 K6 I7 R9 L10 R11 K12 F14 R23 R24 K25 Y28 H35 K36 Y38 R39 Y42 R43 I46 R47 M48 R50 M51 R53 K54 R73 G74 I75 N76 G77 P80 K81 K84 L88 R90 I94 K104 A105 N108 M109 N123 L124 K125 N128 R134 K138 K142 R143 T150 A153 G157 I162 E165 K179 N183 K189 L190 S191 S192 P193 R194 G195 G196 M197 K199 K200 R219

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6p5n, PDBe:6p5n, PDBj:6p5n
• PDBsum: 6p5n
• PubMed: 31609474
• UniProt: G1SV32|RL7_RABIT Large ribosomal subunit protein uL30 (Gene Name=RPL7)