Structure of PDB 5juu Chain UA Binding Site BS01

Receptor Information

>5juu Chain UA (length=91) Species: 4932 (Saccharomyces cerevisiae)

AKRTKKVGITGKYGVRYGSSLRRQVKKLEIQQHARYDCSFCGKKTVKRGA
AGIWTCSCCKKTVAGGAYTVSTAAAATVRSTIRRLREMVEA

Ligand information

>5juu Chain B (length=3307)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaugguguuuugug
cgcauuucacugggccagcaucaguuuugguggcaggauaaauccauagg
aauguagcuugccucgguaaguauuauagccugugggaauacugccagcu
gggacugaggacugcgacguaagucaaggaugcuggcauaaugguuauau
gccgcccgucuugaaacacggaccaaggagucuaacgucuaugcgagugu
uuggguguaaaacccauacgcguaaugaaagugaacguagguuggggccu
cgcaagaggugcacaaucgaccgauccugaugucuucggauggauuugag
uaagagcauagcuguugggacccgaaagauggugaacuaugccugaauag
ggugaagccagaggaaacucugguggaggcucguagcgguucugacgugc
aaaucgaucgucgaauuuggguauaggggcgaaagacuaaucgaaccauc
uaguagcugguuccugccgaaguuucccucaggauagcagaagcucguau
caguuuuaugagguaaagcgaaugauuagagguuccggggucgaaaugac
cuugaccuauucucaaacuuuaaauauguaagaaguccuuguuacuuaau
ugaacguggacauuugaaugaagagcuuuuagugggccauuuuugguaag
cagaacuggcgaugcgggaugaaccgaacguagaguuaaggugccggaau
acacgcucaucagacaccacaaaagguguuaguucaucuagacagccgga
cgguggccauggaagucggaauccgcuaaggaguguguaacaacucaccg
gccgaaugaacuagcccugaaaauggauggcgcucaagcguguuaccuau
acucuaccgucaggguugauaugaugcccugacgaguaggcaggcgugga
ggucagugacgaagccuagaccguaaggucgggucgaacggccucuagug
cagaucuuggugguaguagcaaauauucaaaugagaacuuugaagacuga
aguggggaaagguuccacgucaacagcaguuggacguggguuagucgauc
cuaagagauggggaagcuccguuucaaaggccugauuuuaugcaggccac
caucgaaagggaauccgguuaagauuccggaaccuggauauggauucuuc
acgguaacguaacugaauguggagacgucggcgcgagcccugggaggagu
uaucuuuucuucuuaacagcuuaucaccccggaauugguuuauccggaga
uggggucuuauggcuggaagaggccagcaccuuugcuggcuccggugcgc
uugugacggcccgugaaaauccacaggaaggaauaguuuucaugccaggu
cguacugauaaccgcagcaggucuccaaggugaacagccucuaguugaua
gaauaauguagauaagggaagucggcaaaauagauccguaacuucgggau
aaggauuggcucuaagggucggguagugagggccuuggucagacgcagcg
ggccuuguuguagacggccuugguaggucucuuguagaccgucgcuugcu
acaacgaucaacuuagaacugguacggacaaggggaaucugacugucuaa
uuaaaacauagcauugcgauggucagaaagugauguugacgcaaugugau
uucugcccagugcucugaaugucaaagugaagaaauucaaccaagcgcgg
guaaacggcgggaguaacuaugacucucuuaagguagccaaaugccucgu
caucuaauuagugacgcgcaugaauggauuaacgagauucccacuguccc
uaucuacuaucuagcgaaaccacagccaagggaacgggcuuggcagaauc
agcggggaaagaagacccuguugagcuugacucuaguuugacauugugaa
gagacauagaggguguagaauaagugggagcuucggcgccagugaaauac
cacuaccuuuauaguuucuuuacuuauucaaugaagcggagcuggaauuc
auuuuccacguucuagcauucaaggucccauucggggcugauccggguug
aagacauugucagguggggaguuuggcuggggcggcacaucuguuaaacg
auaacgcagauguccuaaggggggcucauggagaacagaaaucuccagua
gaacaaaaggguaaaagcccccuugauuuugauuuucagugugaauacaa
accaugaaaguguggccuaucgauccuuuagucccucggaauuugaggcu
agaggugccagaaaaguuaccacagggauaacuggcuuguggcagucaag
cguucauagcgacauugcuuuuugauucuucgaugucggcucuuccuauc
auaccgaagcagaauucgguaagcguuggauuguucacccacuaauaggg
aacgugagcuggguuuagaccgucgugagacagguuaguuuuacccuacu
gaugaauguuaccgcaauaguaauugaacuuaguacgagaggaacaguuc
auucggauaauugguuuuugcggcugucugaucaggcauugccgcgaagc
uaccauccgcuggauuauggcugaacgccucuaagucagaauccaugcua
gaacgcggugauuucuuugcuccacacaauauagauggauacgaauaagg
cguccuuguggcgucgcugaaccauagcaggcuagcaacggugcacuugg
cggaaaggccuugggugcuugcuggcgaauugcaaugucauuuugcgugg
ggauaaaucauuuguauacgacuuagauguacaacgggguauuguaagca
guagaguagccuuguuguuacgaucugcugagauuaagccuuuguugucu
gauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5juu 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): A2 R4 T5 K6 K7 V8 G9 I10 G12 K13 Y14 G15 V16 R17 Y18 G19 S20 S21 L22 R23 R36 C42 K44 K48 R49 A51 Y69
• Binding residue (residue number reindexed from 1): A1 R3 T4 K5 K6 V7 G8 I9 G11 K12 Y13 G14 V15 R16 Y17 G18 S19 S20 L21 R22 R35 C41 K43 K47 R48 A50 Y68

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0046872 metal ion binding
• GO:0070180 large ribosomal subunit rRNA binding

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:0044391 ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5juu, PDBe:5juu, PDBj:5juu
• PDBsum: 5juu
• PubMed: 27159452
• UniProt: P0CX25|RL43A_YEAST Large ribosomal subunit protein eL43A (Gene Name=RPL43A)