Structure of PDB 5jus Chain Y Binding Site BS01

Receptor Information

>5jus Chain Y (length=159) Species: 4932 (Saccharomyces cerevisiae)

GKSHGYRSRTRYMFQRDFRKHGAVHLSTYLKVYKVGDIVDIKANGSIQKG
MPHKFYQGKTGVVYNVTKSSVGVIINKMVGNRYLEKRLNLRVEHIKHSKC
RQEFLERVKANAAKRAEAKAQGVAVQLKRQPAQPRESRIVSTEGNVPQTL
APVPYETFI

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

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

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): G2 K3 S4 H5 G6 Y7 R8 R10 R12 Y13 R17 F19 G23 K35 Q49 K50 G51 H54 K55 Y57 Q58 G59 T61 T68 K69 S71 N77 K78 N82 Y84 K87 R88 L89 N90 R92 C101 F105 L106 V109 N112 R116 K120 V126 Q127 L128 K129 R130 Q131 P132
• Binding residue (residue number reindexed from 1): G1 K2 S3 H4 G5 Y6 R7 R9 R11 Y12 R16 F18 G22 K34 Q48 K49 G50 H53 K54 Y56 Q57 G58 T60 T67 K68 S70 N76 K77 N81 Y83 K86 R87 L88 N89 R91 C100 F104 L105 V108 N111 R115 K119 V125 Q126 L127 K128 R129 Q130 P131

Gene Ontology

Molecular Function

• 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:5jus, PDBe:5jus, PDBj:5jus
• PDBsum: 5jus
• PubMed: 27159452
• UniProt: Q02753|RL21A_YEAST Large ribosomal subunit protein eL21A (Gene Name=RPL21A)