Structure of PDB 5juo Chain E Binding Site BS01

Receptor Information

>5juo Chain E (length=171) Species: 4932 (Saccharomyces cerevisiae)

MSKITSSQVREHVKELLKYSNETKKRNFLETVELQVSICIFGDAFDVDRA
KSCGVDAMSVDDLKKLNKNKKLIKKLSKKYNAFIASEVLIKQVPRLLGPQ
LSKAGKFPTPVSHNDDLYGKVTDVRVEMEEDVLVNQILMSVNFFVSLLKK
NWQNVGSLVVKSSMGPAFRLY

Ligand information

>5juo 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: 5juo 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): R26 N27 F28 L29 T31 K97 K98 K101 K102 K105 K106 K130 F190 L194 V205 K207
• Binding residue (residue number reindexed from 1): R26 N27 F28 L29 T31 K70 K71 K74 K75 K78 K79 K103 F144 L148 V159 K161

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000055 ribosomal large subunit export from nucleus
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042254 ribosome biogenesis

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5juo, PDBe:5juo, PDBj:5juo
• PDBsum: 5juo
• PubMed: 27159452
• UniProt: P0CX43|RL1A_YEAST Large ribosomal subunit protein uL1A (Gene Name=RPL1A)