Structure of PDB 5jup Chain I Binding Site BS01

Receptor Information

>5jup Chain I (length=296) Species: 4932 (Saccharomyces cerevisiae)

AFQKDAKSSAYSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYRL
VVRFTNKDIICQIISSTITGDVVLAAAYSHELPRYGITHGLTNWAAAYAT
GLLIARRTLQKLGLDETYKGVEEVEGEYELTEAVEDGPRPFKVFLDIGLQ
RTTTGARVFGALKGASDGGLYVPHSENRFPGWDFETEEIDPELLRSYIFG
GHVSQYMEELADDDEERFSELFKGYLADDIDADSLEDIYTSAHEAIRADP
AFKPTEKKFTKEQYAAESKKYRQTKLSKEERAARVAAKIAALAGQQ

Ligand information

>5jup 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: 5jup Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome.
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): K8 A11 Y12 R15 F16 Q17 R23 G26 T28 D29 Y31 Q32 R35 L36 K43 Y44 T46 L113 P139 R140 P141 F142 F145 L146 I148 L150 R152 T153 F160 P174 H175 S176 N178 R179
• Binding residue (residue number reindexed from 1): K7 A10 Y11 R14 F15 Q16 R22 G25 T27 D28 Y30 Q31 R34 L35 K42 Y43 T45 L112 P138 R139 P140 F141 F144 L145 I147 L149 R151 T152 F159 P173 H174 S175 N177 R178

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0008097 5S rRNA binding
• 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:5jup, PDBe:5jup, PDBj:5jup
• PDBsum: 5jup
• PubMed: 27159452
• UniProt: P26321|RL5_YEAST Large ribosomal subunit protein uL18 (Gene Name=RPL5)