Structure of PDB 7a01 Chain U2 Binding Site BS01

Receptor Information

>7a01 Chain U2 (length=225) Species: 9986 (Oryctolagus cuniculus)

NFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKEYRQMYRTEIRMAR
MARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGTFV
KLNKASINMLRIVEPYIAWGYPNLKSVNELIYKRGYGKINKKRIALTDNT
LIARSLGKYNIICMEDLIHEIYTVGKHFKEANNFLWPFKLSSPRGGMKKK
TTHFVEGGDAGNREDQINRLIRRMN

Ligand information

>7a01 Chain e2 (length=3825)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgg
cccggcggaucuuucccgccccccguggggucggcgggggaccguccccc
gaccggcgaccggccgccgccgggcgcauuuccaccgcggcggugcgccg
cgaccggcuccgggacggcugggaaggcccggcggggaagguggcucggc
ccgaguguuacagcccccccggcagcagcacucgccgaaucccggggccg
agggagcgagacccgucgccgcgcucuccccccucggcgucuccucgugg
gggggccgggccaccccucccacggcgcgaccgcucucccaccccucguc
ggggggcggggcggacuguccccagugcgccccgggcgggucgcgccguc
gggcccgggggagguucucucggggccacgcgcgcgucccccgaagaggg
ggacggcggagcgagcgcacggggucggcggcgacgucggcuacccaccc
gacccgucuugaaacacggaccaaggagucuaacacgugcgcgagucggg
ggcucgcacgaaagccgccguggcgcaaugaaggugaaggccggcgcgcu
cgccggccgaggugggaucccgaggccucuccaguccgccgagggcgcac
caccggcccgucucgcccgccgcgccggggagguggagcacgagcgcacg
uguuaggacccgaaagauggugaacuaugccugggcagggcgaagccaga
ggaaacucugguggagguccguagcgguccugacgugcaaaucggucguc
cgaccuggguauaggggcgaaagacuaaucgaaccaucuaguagcugguu
cccuccgaaguuucccucaggauagcuggcgcucucgcagacccgacgca
cccccgccacgcaguuuuauccgguaaagcgaaugauuagaggucuuggg
gccgaaacgaucucaaccuauucucaaacuuuaaauggguaagaagcccg
gcucgcuggcgugagccgggcguggaauggagugccuagugggccacuuu
ugguaagcagaacuggcgcugcgggaugaaccgaacgccggguuaaggcg
cccgaugccgacgcucaucagaccccagaaaagguguugguugauauaga
cagcaggacgguggccauggaagucggaauccgcuaaggaguguguaaca
acucaccugccgaaucaacuagcccugaaaauggauggcgcuggagcguc
gggcccauacccggccgucgccggcagucgagaguggacgggagcggcgg
gggcggcgcgcgcgcgcgcccgcccccggagccccgcggacgcuacgccg
cgacgaguaggagggccgcugcggugagccuugaagccuagggcgcgggc
ccggguggagccgccgcaggugcagaucuuggugguaguagcaaauauuc
aaacgagaacuuugaaggccgaaguggagaaggguuccaugugaacagca
guugaacaugggucagucgguccugagagaugggcgagcgccguuccgaa
gggacgggcgauggccuccguugcccucggccgaucgaaagggagucggg
uucagauccccgaauccggaguggcggagaugggcgccgcgaggcgucca
gugcgguaacgcgaccgaucccggagaagccggcgggagccccggggaga
guucucuuuucuuugugaagggcagggcgcccuggaauggguucgccccg
agagaggggcccgugccuuggaaagcgucgcgguuccggcggcguccggu
gagcucucgcuggcccuugaaaauccgggggagaggguguaaaucucgcg
ccgggccguacccauauccgcagcaggucuccaaggugaacagccucugg
cauguuggaacaauguagguaagggaagucggcaagccggauccguaacu
ucgggauaaggauuggcucuaagggcugcagccgacuuagaacuggugcg
gaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaaggcccg
cggcggguguugacgcgaugugauuucugcccagugcucugaaugucaaa
gugaagaaauucaaugaagcgcggguaaacggcgggaguaacuaugacuc
ucuuaagguagccaaaugccucgucaucuaauuagugacgcgcaugaaug
gaugaacgagauucccacugucccuaccuacuauccagcgaaaccacagc
caagggaacgggcuuggcggaaucagcggggaaagaagacccuguugagc
uugacucuagucuggcacggugaagagacaugagagguguagaauaagug
ggaggcccccggcgcccccccgguguccccgcgaggggcccggggcgggg
uccgccggcccugcgggccgccggugaaauaccacuacucugaucguuuu
uucacugacccggugaggcgggggggcgagccccgaggggcucucgcuuc
uggcgccaagcgcccggccgcgcgccggccgggcgcgacccgcuccgggg
acagugccagguggggaguuugacuggggcgguacaccugucaaacggua
acgcagguguccuaaggcgagcucagggaggacagaaaccucccguggag
cagaagggcaaaagcucgcuugaucuugauuuucaguacgaauacagacc
gugaaagcggggccucacgauccuucugaccuuuuggguuuuaagcagga
ggugucagaaaaguuaccacagggauaacuggcuuguggcggccaagcgu
ucauagcgacgucgcuuuuugauccuucgaugucggcucuuccuaucauu
gugaagcagaauucaccaagcguuggauuguucacccacuaauagggaac
gugagcuggguuuagaccgucgugagacagguuaguuuuacccuacugau
gauguguuguugccaugguaauccugcucaguacgagaggaaccgcaggu
ucagacauuugguguaugugcuuggcugaggagccaauggggcgaagcua
ccaucugugggauuaugacugaacgccucuaagucagaaucccgcccagg
cggaacgauacggcagcgccgcggagccucgguuggccucggauagccgg
ucccccgccgggaccgggguccggugcggagugcccuucguccugggaaa
cggggcgcggccggagaggcggccgcccccucgcccgucacgcaccggcc
guucguggggaaccuggcgcuaaaccauucguagacgaccugcuucuggg
ucgggguuucguacguagcagagcagcucccucgcugcgaucuauugaaa
gucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7a01 The Halastavi arva Virus Intergenic Region IRES Promotes Translation by the Simplest Possible Initiation Mechanism.
• Resolution: 3.6 Å
• Binding residue (original residue number in PDB): N23 F24 K28 K30 R31 L32 R33 K34 F36 Q38 M40 L41 R42 K43 R45 R46 L48 Y50 E51 K52 H57 K58 Y60 R61 Y64 R65 R72 M73 R75 R95 G96 I97 N98 G99 P102 K103 K106 L110 I116 K126 N130 M131 L146 K147 N150 K160 K164 R165 D170 T172 R176 G179 K180 E187 K201 N205 K211 S213 S214 P215 G217 M219 K220 K221 K222 R241 R244
• Binding residue (residue number reindexed from 1): N1 F2 K6 K8 R9 L10 R11 K12 F14 Q16 M18 L19 R20 K21 R23 R24 L26 Y28 E29 K30 H35 K36 Y38 R39 Y42 R43 R50 M51 R53 R73 G74 I75 N76 G77 P80 K81 K84 L88 I94 K104 N108 M109 L124 K125 N128 K138 K142 R143 D148 T150 R154 G157 K158 E165 K179 N183 K189 S191 S192 P193 G195 M197 K198 K199 K200 R219 R222

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:7a01, PDBe:7a01, PDBj:7a01
• PDBsum: 7a01
• PubMed: 33296660
• UniProt: G1SV32|RL7_RABIT Large ribosomal subunit protein uL30 (Gene Name=RPL7)