Structure of PDB 7a01 Chain S2 Binding Site BS01

Receptor Information

>7a01 Chain S2 (length=187) Species: 9986 (Oryctolagus cuniculus)

GVDIRHNKDRKVRRKEPKSQDIYLRLLVKLYRFLARRTNSTFNQVVLKRL
FMSRTNRPPLSLSRMIRKMKLPGRENKTAVVVGTITDDVRVQEVPKLKVC
ALRVTSRARSRILRAGGKILTFDQLALDSPKGCGTVLLSGPRKGREVYRH
FGKAPGTPHSHTKPYVRSKGRKFERARGRRASRGYKN

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): G2 R11 K12 V13 R14 R15 K19 Q21 R26 K30 R37 R38 N40 T42 F43 M53 S54 R55 T56 S62 S64 R65 K69 R75 K78 T87 D89 R91 T106 C134 G135 L139 S140 P142 R143 K144 G145 R146 V148 R150 F152 P159 H160 H162 T163 K164 Y166 S169 K170 R172 K173 F174 E175 R178 R181 S183 R184 G185 Y186
• Binding residue (residue number reindexed from 1): G1 R10 K11 V12 R13 R14 K18 Q20 R25 K29 R36 R37 N39 T41 F42 M52 S53 R54 T55 S61 S63 R64 K68 R74 K77 T86 D88 R90 T105 C133 G134 L138 S139 P141 R142 K143 G144 R145 V147 R149 F151 P158 H159 H161 T162 K163 Y165 S168 K169 R171 K172 F173 E174 R177 R180 S182 R183 G184 Y185

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

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005791 rough endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0043232 intracellular non-membrane-bounded organelle
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7a01, PDBe:7a01, PDBj:7a01
• PDBsum: 7a01
• PubMed: 33296660
• UniProt: Q07020|RL18_HUMAN Large ribosomal subunit protein eL18 (Gene Name=RPL18)