Structure of PDB 5juu Chain Q Binding Site BS01

Receptor Information

>5juu Chain Q (length=193) Species: 4932 (Saccharomyces cerevisiae)

AISKNLPILKNHFRKHWQERVKVHFDQAGKKVSRRNARATRAAKIAPRPL
DLLRPVVRAPTVKYNRKVRAGRGFTLAEVKAAGLTAAYARTIGIAVDHRR
QNRNQEIFDANVQRLKEYQSKIIVFPRNGKAPEAEQVLSAAATFPIAQPA
TDVEARAVQDNGESAFRTLRLARSEKKFRGIREKRAREKAEAE

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 K5 L7 P8 L10 K11 H13 F14 R15 K16 W18 Q19 K23 Q28 K32 R35 R36 R39 R42 R55 V58 R59 P61 T62 Y65 N66 R70 R73 L77 K81 T86 R91 D98 H99 R100 R101 Q102 R104 N105 R128 G130 R171 R174 S175 K178 F179 I182 R183 R186
• Binding residue (residue number reindexed from 1): A1 K4 L6 P7 L9 K10 H12 F13 R14 K15 W17 Q18 K22 Q27 K31 R34 R35 R38 R41 R54 V57 R58 P60 T61 Y64 N65 R69 R72 L76 K80 T85 R90 D97 H98 R99 R100 Q101 R103 N104 R127 G129 R170 R173 S174 K177 F178 I181 R182 R185

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:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5juu, PDBe:5juu, PDBj:5juu
• PDBsum: 5juu
• PubMed: 27159452
• UniProt: Q12690|RL13A_YEAST Large ribosomal subunit protein eL13A (Gene Name=RPL13A)