Structure of PDB 5juu Chain G Binding Site BS01

Receptor Information

>5juu Chain G (length=386) Species: 4932 (Saccharomyces cerevisiae)

SHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKA
GMTTIVRDLDRPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRS
LTTVWAEHLSDEVKRRFYKNWYKSKKKAFTKYSAKYAQDGAGIERELARI
KKYASVVRVLVHTQIRKTPLAQKKAHLAEIQLNGGSISEKVDWAREHFEK
TVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPRKTHRGLRKVAC
IGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDRT
KKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKAL
EEVSLKWIDTASKFGKGRFQTPAEKHAFMGTLKKDL

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): S2 H3 R4 K5 E7 A8 P9 R10 H11 G12 H13 L14 G15 F16 L17 P18 R19 K20 R21 I25 R26 K30 A31 M53 T54 T55 R62 G64 S65 E74 A75 Y92 T95 R97 G98 L99 R100 S101 L102 T103 T104 R116 R117 F118 Y119 K120 N121 Y123 K124 K126 K128 F130 K132 Y133 R150 Y154 R159 P170 Q173 K174 K175 H177 A179 E180 T221 K222 G223 H224 G225 F226 E227 G228 K236 K237 L238 R240 K241 T242 H243 R244 L246 R247 K248 V249 A250 C251 I252 G253 A254 W255 H256 P257 A258 H259 V260 M261 W262 S263 V264 R266 Q269 R270 Y272 S274 R275 T276 I278 N279 M308 G309 H313 Y314 G315 E316 K325 G326 C327 P329 N331 R332 K333 R334 L342 Y343 R348 S363 K364 F365 G366 K367 K376 F379 M380 L383 K384
• Binding residue (residue number reindexed from 1): S1 H2 R3 K4 E6 A7 P8 R9 H10 G11 H12 L13 G14 F15 L16 P17 R18 K19 R20 I24 R25 K29 A30 M52 T53 T54 R61 G63 S64 E73 A74 Y91 T94 R96 G97 L98 R99 S100 L101 T102 T103 R115 R116 F117 Y118 K119 N120 Y122 K123 K125 K127 F129 K131 Y132 R149 Y153 R158 P169 Q172 K173 K174 H176 A178 E179 T220 K221 G222 H223 G224 F225 E226 G227 K235 K236 L237 R239 K240 T241 H242 R243 L245 R246 K247 V248 A249 C250 I251 G252 A253 W254 H255 P256 A257 H258 V259 M260 W261 S262 V263 R265 Q268 R269 Y271 S273 R274 T275 I277 N278 M307 G308 H312 Y313 G314 E315 K324 G325 C326 P328 N330 R331 K332 R333 L341 Y342 R347 S362 K363 F364 G365 K366 K375 F378 M379 L382 K383

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0006414 translational elongation
• GO:1990145 maintenance of translational fidelity

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: P14126|RL3_YEAST Large ribosomal subunit protein uL3 (Gene Name=RPL3)