Structure of PDB 3j6x Chain 55 Binding Site BS01

Receptor Information

>3j6x Chain 55 (length=203) Species: 580240 (Saccharomyces cerevisiae W303)

GAYKYLEELQRKKQSDVLRFLQRVRVWEYRQKNVIHRAARPTRPDKARRL
GYKAKQGFVIYRVRVRRGNRKRPVPKGATYGKPTNQGVNELKYQRSLRAT
AEERVGRRAANLRVLNSYWVNQDSTYKYFEVILVDPQHKAIRRDARYNWI
CDPVHKHREARGLTATGKKSRGINKGHKFNNTKAGRRKTWKRQNTLSLWR
YRK

Ligand information

>3j6x Chain 2S (length=3308)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaugguguuuugug
cucgcauuucacuggccagcaucaguuuugguggcaggauaaauccauag
gaauguagcuugccucgguaaguauuauagccugugggaauacugccagc
ugggacugaggacugcgacguaagucaaggaugcuggcauaaugguuaua
ugccgcccgucuugaaacacggaccaaggagucuaacgucuaugcgagug
uuuggguguaaaacccauacgcguaaugaaagugaacguagguuggggcc
ucgcaagaggugcacaaucgaccgauccugaugucuucggauggauuuga
guaagagcauagcuguugggacccgaaagauggugaacuaugccugaaua
gggugaagccagaggaaacucugguggaggcucguagcgguucugacgug
caaaucgaucgucgaauuuggguauaggggcgaaagacuaaucgaaccau
cuaguagcugguuccugccgaaguuucccucaggauagcagaagcucgua
ucaguuuuaugagguaaagcgaaugauuagagguuccggggucgaaauga
ccuugaccuauucucaaacuuuaaauauguaagaaguccuuguuacuuaa
uugaacguggacauuugaaugaagagcuuuuagugggccauuuuugguaa
gcagaacuggcgaugcgggaugaaccgaacguagaguuaaggugccggaa
uacacgcucaucagacaccacaaaagguguuaguucaucuagacagccgg
acgguggccauggaagucggaauccgcuaaggaguguguaacaacucacc
ggccgaaugaacuagcccugaaaauggauggcgcucaagcguguuaccua
uacucuaccgucaggguugauaugaugcccugacgaguaggcaggcgugg
aggucagugacgaagccuagaccguaaggucgggucgaacggccucuagu
gcagaucuuggugguaguagcaaauauucaaaugagaacuuugaagacug
aaguggggaaagguuccacgucaacagcaguuggacguggguuagucgau
ccuaagagauggggaagcuccguuucaaaggccugauuuuaugcaggcca
ccaucgaaagggaauccgguuaagauuccggaaccuggauauggauucuu
cacgguaacguaacugaauguggagacgucggcgcgagcccugggaggag
uuaucuuuucuucuuaacagcuuaucaccccggaauugguuuauccggag
auggggucuuauggcuggaagaggccagcaccuuugcuggcuccggugcg
cuugugacggcccgugaaaauccacaggaaggaauaguuuucaugccagg
ucguacugauaaccgcagcaggucuccaaggugaacagccucuaguugau
agaauaauguagauaagggaagucggcaaaauagauccguaacuucggga
uaaggauuggcucuaagggucggguagugagggccuuggucagacgcagc
gggccuuguuguagacggccuugguaggucucuuguagaccgucgcuugc
uacaacgaucaacuuagaacugguacggacaaggggaaucugacugucua
auuaaaacauagcauugcgauggucagaaagugauguugacgcaauguga
uuucugcccagugcucugaaugucaaagugaagaaauucaaccaagcgcg
gguaaacggcgggaguaacuaugacucucuuaagguagccaaaugccucg
ucaucuaauuagugacgcgcaugaauggauuaacgagauucccacugucc
cuaucuacuaucuagcgaaaccacagccaagggaacgggcuuggcagaau
cagcggggaaagaagacccuguugagcuugacucuaguuugacauuguga
agagacauagaggguguagaauaagugggagcuucggcgccagugaaaua
ccacuaccuuuauaguuucuuuacuuauucaaugaagcggagcuggaauu
cauuuuccacguucuagcauucaaggucccauucggggcugauccggguu
gaagacauugucagguggggaguuuggcuggggcggcacaucuguuaaac
gauaacgcagauguccuaaggggggcucauggagaacagaaaucuccagu
agaacaaaaggguaaaagcccccuugauuuugauuuucagugugaauaca
aaccaugaaaguguggccuaucgauccuuuagucccucggaauuugaggc
uagaggugccagaaaaguuaccacagggauaacuggcuuguggcagucaa
gcguucauagcgacauugcuuuuugauucuucgaugucggcucuuccuau
cauaccgaagcagaauucgguaagcguuggauuguucacccacuaauagg
gaacgugagcuggguuuagaccgucgugagacagguuaguuuuacccuac
ugaugaauguuaccgcaauaguaauugaacuuaguacgagaggaacaguu
cauucggauaauugguuuuugcggcugucugaucaggcauugccgcgaag
cuaccauccgcuggauuauggcugaacgccucuaagucagaauccaugcu
agaacgcggugauuucuuugcuccacacaauauagauggauacgaauaag
gcguccuuguggcgucgcugaaccauagcaggcuagcaacggugcacuug
gcggaaaggccuugggugcuugcuggcgaauugcaaugucauuuugcgug
gggauaaaucauuuguauacgacuuagauguacaacgggguauuguaagc
aguagaguagccuuguuguuacgaucugcugagauuaagccuuuguuguc
ugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3j6x Taura syndrome virus IRES initiates translation by binding its tRNA-mRNA-like structural element in the ribosomal decoding center.
• Resolution: 6.1 Å
• Binding residue (original residue number in PDB): K5 E8 R12 K14 Q15 R24 W28 R31 N34 V35 A40 R41 R44 R49 R50 L51 K54 A55 R67 R68 G69 N70 R71 K72 K77 Y81 G82 K83 P84 T85 Q87 V89 N90 E91 K93 Y94 Q95 R96 S97 L98 R105 R108 A111 N112 W120 S125 Q138 K140 A141 R147 W150 P154 K157 H158 A161 R162 A166 K169 K170 S171 R172 I174 K176 G177 H178 K179 N182 R187 R188 K189 W191 R193 Q194 W200 Y202 R203
• Binding residue (residue number reindexed from 1): K4 E7 R11 K13 Q14 R23 W27 R30 N33 V34 A39 R40 R43 R48 R49 L50 K53 A54 R66 R67 G68 N69 R70 K71 K76 Y80 G81 K82 P83 T84 Q86 V88 N89 E90 K92 Y93 Q94 R95 S96 L97 R104 R107 A110 N111 W119 S124 Q137 K139 A140 R146 W149 P153 K156 H157 A160 R161 A165 K168 K169 S170 R171 I173 K175 G176 H177 K178 N181 R186 R187 K188 W190 R192 Q193 W199 Y201 R202

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:3j6x, PDBe:3j6x, PDBj:3j6x
• PDBsum: 3j6x
• PubMed: 24927574
• UniProt: P05748|RL15A_YEAST Large ribosomal subunit protein eL15A (Gene Name=RPL15A)