Structure of PDB 5jus Chain H Binding Site BS01

Receptor Information

>5jus Chain H (length=361) Species: 4932 (Saccharomyces cerevisiae)

SRPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYA
VSEKAGHQTSAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFA
PTKTWRKWNVKVNHNEKRYATASAIAATAVASLVLARGHRVEKIPEIPLV
VSTDLESIQKTKEAVAALKAVGAHSDLLKVLKSKKLRAGKGKYRNRRWTQ
RRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAPGAHLGRFVIWT
EAAFTKLDQVWGSETVASSKVGYTLPSHIISTSDVTRIINSSEIQSAIRP
AGQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKLGSKKAEKTGTKP
AAVFTETLKHD

Ligand information

>5jus 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

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5jus Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome.
• Resolution: 4.2 Å
• Binding residue (original residue number in PDB): V42 K44 N45 K46 R47 Q48 Y50 S53 E54 A56 H58 Q59 T60 S61 E63 S64 T67 G68 A70 V71 A72 R73 I74 P75 V77 G80 G81 T82 G83 R84 Q87 G88 F90 N92 M93 R95 G96 G97 R98 M99 F100 A101 P102 K104 W106 R107 K108 V111 K112 V113 N114 H115 N116 E117 K118 R119 Y120 R141 T162 K163 L179 K180 L182 S184 K185 K186 L187 R188 K191 G192 R195 N196 R197 R198 W199 R202 R203 K217 R220 N221 P223 T227 N234 P240 H243 K271 V272 T275 A302 G303 Q307 K308 R309 V312 L313 K314 K315 N316 L318 K319 N320 Q322 L324 L325 R326 N328 Y330 A331 K332 F334 G340 S341 K342 K343 A344 T347 T349 T356
• Binding residue (residue number reindexed from 1): V41 K43 N44 K45 R46 Q47 Y49 S52 E53 A55 H57 Q58 T59 S60 E62 S63 T66 G67 A69 V70 A71 R72 I73 P74 V76 G79 G80 T81 G82 R83 Q86 G87 F89 N91 M92 R94 G95 G96 R97 M98 F99 A100 P101 K103 W105 R106 K107 V110 K111 V112 N113 H114 N115 E116 K117 R118 Y119 R140 T161 K162 L178 K179 L181 S183 K184 K185 L186 R187 K190 G191 R194 N195 R196 R197 W198 R201 R202 K216 R219 N220 P222 T226 N233 P239 H242 K270 V271 T274 A301 G302 Q306 K307 R308 V311 L312 K313 K314 N315 L317 K318 N319 Q321 L323 L324 R325 N327 Y329 A330 K331 F333 G339 S340 K341 K342 A343 T346 T348 T355

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: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:5jus, PDBe:5jus, PDBj:5jus
• PDBsum: 5jus
• PubMed: 27159452
• UniProt: P10664|RL4A_YEAST Large ribosomal subunit protein uL4A (Gene Name=RPL4A)