Structure of PDB 5juu Chain DA Binding Site BS01

Receptor Information

>5juu Chain DA (length=126) Species: 4932 (Saccharomyces cerevisiae)

AKQSLDVSSDRRKARKAYFTAPSSQRRVLLSAPLSKELRAQYGIKALPIR
RDDEVLVVRGSKKGQEGKISSVYRLKFAVQVDKVTKEKVNGASVPINLHP
SKLVITKLHLDKDRKALIQRKGGKLE

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): A2 K3 Q4 V8 S9 S10 R12 K14 R16 L30 S32 P34 K46 A47 V59 R60 G61 S62 K77 K87 K89 V90 H100 S102 K103 R121 K122
• Binding residue (residue number reindexed from 1): A1 K2 Q3 V7 S8 S9 R11 K13 R15 L29 S31 P33 K45 A46 V58 R59 G60 S61 K76 K86 K88 V89 H99 S101 K102 R120 K121

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:0032991 protein-containing complex
• GO:0043232 intracellular non-membrane-bounded organelle
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5juu, PDBe:5juu, PDBj:5juu
• PDBsum: 5juu
• PubMed: 27159452
• UniProt: P05743|RL26A_YEAST Large ribosomal subunit protein uL24A (Gene Name=RPL26A)