Structure of PDB 3j6y Chain 55 Binding Site BS01

Receptor Information

>3j6y Chain 55 (length=203) Species: 580240 (Saccharomyces cerevisiae W303)

GAYKYLEELQRKKQSDVLRFLQRVRVWEYRQKNVIHRAARPTRPDKARRL
GYKAKQGFVIYRVRVRRGNRKRPVPKGATYGKPTNQGVNELKYQRSLRAT
AEERVGRRAANLRVLNSYWVNQDSTYKYFEVILVDPQHKAIRRDARYNWI
CDPVHKHREARGLTATGKKSRGINKGHKFNNTKAGRRKTWKRQNTLSLWR
YRK

Ligand information

>3j6y 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: 3j6y 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): G2 Y4 K5 R12 K14 W28 R31 N34 V35 R41 R44 K47 R49 R50 K54 A55 Q57 R67 R68 G69 N70 R71 K72 R73 P74 P76 K77 Y81 K83 P84 T85 Q87 V89 N90 E91 K93 Y94 Q95 R96 S97 L98 R105 R108 N112 W120 S125 Q138 R147 W150 P154 H156 H158 R159 A161 A166 K169 K170 S171 R172 I174 K176 G177 H178 K179 F180 N181 N182 R187 R188 W191 R193 Q194 W200 R201 Y202 R203 K204
• Binding residue (residue number reindexed from 1): G1 Y3 K4 R11 K13 W27 R30 N33 V34 R40 R43 K46 R48 R49 K53 A54 Q56 R66 R67 G68 N69 R70 K71 R72 P73 P75 K76 Y80 K82 P83 T84 Q86 V88 N89 E90 K92 Y93 Q94 R95 S96 L97 R104 R107 N111 W119 S124 Q137 R146 W149 P153 H155 H157 R158 A160 A165 K168 K169 S170 R171 I173 K175 G176 H177 K178 F179 N180 N181 R186 R187 W190 R192 Q193 W199 R200 Y201 R202 K203

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:3j6y, PDBe:3j6y, PDBj:3j6y
• PDBsum: 3j6y
• PubMed: 24927574
• UniProt: P05748|RL15A_YEAST Large ribosomal subunit protein eL15A (Gene Name=RPL15A)