Structure of PDB 5jus Chain AA Binding Site BS02

Receptor Information

>5jus Chain AA (length=136) Species: 4932 (Saccharomyces cerevisiae)

SGNGAQGTKFRISLGLPVGAIMNCADNSGARNLYIIAVKGSGSRLNRLPA
ASLGDMVMATVKKGKPELRKKVMPAIVVRQAKSWRRRDGVFLYFEDNAGV
IANPKGEMKGSAITGPVGKECADLWPRVASNSGVVV

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): G3 Q7 G8 T9 K10 F11 R12 S14 G16 L17 P18 G20 A21 I22 I37 K40 G41 G43 S44 R45 L46 N47 R48 L49 T61 K63 K71 K83 S84 R88 F92
• Binding residue (residue number reindexed from 1): G2 Q6 G7 T8 K9 F10 R11 S13 G15 L16 P17 G19 A20 I21 I36 K39 G40 G42 S43 R44 L45 N46 R47 L48 T60 K62 K70 K82 S83 R87 F91

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0070180 large ribosomal subunit rRNA binding

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: P0CX41|RL23A_YEAST Large ribosomal subunit protein uL14A (Gene Name=RPL23A)