Structure of PDB 5jut Chain O Binding Site BS01

Receptor Information

>5jut Chain O (length=169) Species: 4932 (Saccharomyces cerevisiae)

QNPMRDLKIEKLVLNISVGESGDRLTRASKVLEQLSGQTPVQSKARYTVR
TFGIRRNEKIAVHVTVRGPKAEEILERGLKVKEYQLRDRNFSATGNFGFG
IDEHIDLGIKYDPSIGIFGMDFYVVMNRPGARVTRRKRCKGTVGNSHKTT
KEDTVSWFKQKYDADVLDK

Ligand information

>5jut Chain B (length=3309)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaugguguuuugug
cucgcauuucacugggccagcaucaguuuugguggcaggauaaauccaua
ggaauguagcuugccucgguaaguauuauagccugugggaauacugccag
cugggacugaggacugcgacguaagucaaggaugcuggcauaaugguuau
augccgcccgucuugaaacacggaccaaggagucuaacgucuaugcgagu
guuuggguguaaaacccauacgcguaaugaaagugaacguagguuggggc
cucgcaagaggugcacaaucgaccgauccugaugucuucggauggauuug
aguaagagcauagcuguugggacccgaaagauggugaacuaugccugaau
agggugaagccagaggaaacucugguggaggcucguagcgguucugacgu
gcaaaucgaucgucgaauuuggguauaggggcgaaagacuaaucgaacca
ucuaguagcugguuccugccgaaguuucccucaggauagcagaagcucgu
aucaguuuuaugagguaaagcgaaugauuagagguuccggggucgaaaug
accuugaccuauucucaaacuuuaaauauguaagaaguccuuguuacuua
auugaacguggacauuugaaugaagagcuuuuagugggccauuuuuggua
agcagaacuggcgaugcgggaugaaccgaacguagaguuaaggugccgga
auacacgcucaucagacaccacaaaagguguuaguucaucuagacagccg
gacgguggccauggaagucggaauccgcuaaggaguguguaacaacucac
cggccgaaugaacuagcccugaaaauggauggcgcucaagcguguuaccu
auacucuaccgucaggguugauaugaugcccugacgaguaggcaggcgug
gaggucagugacgaagccuagaccguaaggucgggucgaacggccucuag
ugcagaucuuggugguaguagcaaauauucaaaugagaacuuugaagacu
gaaguggggaaagguuccacgucaacagcaguuggacguggguuagucga
uccuaagagauggggaagcuccguuucaaaggccugauuuuaugcaggcc
accaucgaaagggaauccgguuaagauuccggaaccuggauauggauucu
ucacgguaacguaacugaauguggagacgucggcgcgagcccugggagga
guuaucuuuucuucuuaacagcuuaucaccccggaauugguuuauccgga
gauggggucuuauggcuggaagaggccagcaccuuugcuggcuccggugc
gcuugugacggcccgugaaaauccacaggaaggaauaguuuucaugccag
gucguacugauaaccgcagcaggucuccaaggugaacagccucuaguuga
uagaauaauguagauaagggaagucggcaaaauagauccguaacuucggg
auaaggauuggcucuaagggucggguagugagggccuuggucagacgcag
cgggccuuguuguagacggccuugguaggucucuuguagaccgucgcuug
cuacaacgaucaacuuagaacugguacggacaaggggaaucugacugucu
aauuaaaacauagcauugcgauggucagaaagugauguugacgcaaugug
auuucugcccagugcucugaaugucaaagugaagaaauucaaccaagcgc
ggguaaacggcgggaguaacuaugacucucuuaagguagccaaaugccuc
gucaucuaauuagugacgcgcaugaauggauuaacgagauucccacuguc
ccuaucuacuaucuagcgaaaccacagccaagggaacgggcuuggcagaa
ucagcggggaaagaagacccuguugagcuugacucuaguuugacauugug
aagagacauagaggguguagaauaagugggagcuucggcgccagugaaau
accacuaccuuuauaguuucuuuacuuauucaaugaagcggagcuggaau
ucauuuuccacguucuagcauucaaggucccauucggggcugauccgggu
ugaagacauugucagguggggaguuuggcuggggcggcacaucuguuaaa
cgauaacgcagauguccuaaggggggcucauggagaacagaaaucuccag
uagaacaaaaggguaaaagcccccuugauuuugauuuucagugugaauac
aaaccaugaaaguguggccuaucgauccuuuagucccucggaauuugagg
cuagaggugccagaaaaguuaccacagggauaacuggcuuguggcaguca
agcguucauagcgacauugcuuuuugauucuucgaugucggcucuuccua
ucauaccgaagcagaauucgguaagcguuggauuguucacccacuaauag
ggaacgugagcuggguuuagaccgucgugagacagguuaguuuuacccua
cugaugaauguuaccgcaauaguaauugaacuuaguacgagaggaacagu
ucauucggauaauugguuuuugcggcugucugaucaggcauugccgcgaa
gcuaccauccgcuggauuauggcugaacgccucuaagucagaauccaugc
uagaacgcggugauuucuuugcuccacacaauauagauggauacgaauaa
ggcguccuuguggcgucgcugaaccauagcaggcuagcaacggugcacuu
ggcggaaaggccuugggugcuugcuggcgaauugcaaugucauuuugcgu
ggggauaaaucauuuguauacgacuuagauguacaacgggguauuguaag
caguagaguagccuuguuguuacgaucugcugagauuaagccuuuguugu
cugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5jut Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome.
• Resolution: 4.0 Å
• Binding residue (original residue number in PDB): K16 V18 N20 S22 S48 A50 R51 T56 F57 I65 A66 H68 N95 F96 S97 T99 N101 F104 G105 D107 G124 M125 D126 Y128 K142
• Binding residue (residue number reindexed from 1): K11 V13 N15 S17 S43 A45 R46 T51 F52 I60 A61 H63 N90 F91 S92 T94 N96 F99 G100 D102 G119 M120 D121 Y123 K137

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5jut, PDBe:5jut, PDBj:5jut
• PDBsum: 5jut
• PubMed: 27159452
• UniProt: P0C0W9|RL11A_YEAST Large ribosomal subunit protein uL5A (Gene Name=RPL11A)