Structure of PDB 5jus Chain W Binding Site BS02

Receptor Information

>5jus Chain W (length=188) Species: 4932 (Saccharomyces cerevisiae)

ANLRTQKRLAASVVGVGKRKVWLDPNETSEIAQANSRNAIRKLVKNGTIV
KKAVTVHSKSRTRAHAQSKREGRHSGYGKRKGTREARLPSQVVWIRRLRV
LRRLLAKYRDAGKIDKHLYHVLYKESKGNAFKHKRALVEHIIQAKADAQR
EKALNEEAEARRLKNRAARDRRAQRVAEKRDALLKEDA

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): N3 L4 R5 K8 R9 G18 K19 R20 W23 L24 P26 S37 R38 K43 K46 K53 V55 T56 V57 H58 S59 K60 S61 R62 T63 R64 H66 R74 H75 G77 Y78 G79 K80 R81 K82 G83 T84 R85 R88 L89 Q92 W95 I96 R97 V101 R103 R104 R110 K114 H118 Y120 H121 Y124 K125 E126 K128 N130 K135
• Binding residue (residue number reindexed from 1): N2 L3 R4 K7 R8 G17 K18 R19 W22 L23 P25 S36 R37 K42 K45 K52 V54 T55 V56 H57 S58 K59 S60 R61 T62 R63 H65 R73 H74 G76 Y77 G78 K79 R80 K81 G82 T83 R84 R87 L88 Q91 W94 I95 R96 V100 R102 R103 R109 K113 H117 Y119 H120 Y123 K124 E125 K127 N129 K134

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: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: P0CX82|RL19A_YEAST Large ribosomal subunit protein eL19A (Gene Name=RPL19A)