Structure of PDB 8hfr Chain Jy Binding Site BS01

Receptor Information

>8hfr Chain Jy (length=166) Species: 559292 (Saccharomyces cerevisiae S288C)

PMRDLKIEKLVLNISVGESGDRLTRASKVLEQLSGQTPVQSKARYTVRTF
GIRRNEKIAVHVTVRGPKAEEILERGLKVKEYQLRDRNFSATGNFGFGID
EHIDLGIKYDPSIGIFGMDFYVVMNRPGARVTRRKRCKGTVGNSHKTTKE
DTVSWFKQKYDADVLD

Ligand information

>8hfr Chain 1e (length=3274)

ugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaag
cggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagcg
gcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaauu
uggagagggcaacuuuggggccguuccuugucuauguuccuuggaacagg
acgucauagagggugagaaucccguguggcgaggagugcgguucuuugua
aagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggug
guaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaag
uacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaaguac
gugaaauuguugaaagggaagggcauuugaucagacgccagcaucaguuu
ugguggcaggauaaauccauaggaauguagcuugccucgguaaguauuau
agccugugggaauacugccagcugggacugaggacugcgacguaagucaa
ggaugcuggcauaaugguuauaugccgcccgucuugaaacacggaccaag
gagucuaacgucuaugcgaguguuuggguguaaaacccauacgcguaaug
aaagugaacguagguuggggccucgcaagaggugcacaaucgaccgaucc
ugaugucuucggauggauuugaguaagagcauagcuguugggacccgaaa
gauggugaacuaugccugaauagggugaagccagaggaaacucuggugga
ggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguauagg
ggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguuucc
cucaggauagcagaagcucguaucaguuuuaugagguaaagcgaaugauu
agagguuccggggucgaaaugaccuugaccuauucucaaacuuuaaauau
guaagaaguccuuguuacuuaauugaacguggacauuugaaugaagagcu
uuuagugggccauuuuugguaagcagaacuggcgaugcgggaugaaccga
acguagaguuaaggugccggaauacacgcucaucagacaccacaaaaggu
guuaguucaucuagacagccggacgguggccauggaagucggaauccgcu
aaggaguguguaacaacucaccggccgaaugaacuagcccugaaaaugga
uggcgcucaagcguguuaccuauacucuaccgucaggguugauaugaugc
ccugacgaguaggcaggcguggaggucagugacgaagccuagaccguaag
gucgggucgaacggccucuagugcagaucuuggugguaguagcaaauauu
caaaugagaacuuugaagacugaaguggggaaagguuccacgucaacagc
aguuggacguggguuagucgauccuaagagauggggaagcuccguuucaa
aggccugauuuuaugcaggccaccaucgaaagggaauccgguuaagauuc
cggaaccuggauauggauucuucacgguaacguaacugaauguggagacg
ucggcgcgagcccugggaggaguuaucuuuucuucuuaacagcuuaucac
cccggaauugguuuauccggagauggggucuuauggcuggaagaggccag
caccuuugcuggcuccggugcgcuugugacggcccgugaaaauccacagg
aaggaauaguuuucaugccaggucguacugauaaccgcagcaggucucca
aggugaacagccucuaguugauagaauaauguagauaagggaagucggca
aaauagauccguaacuucgggauaaggauuggcucuaagggucggguagu
gagggccuuggucagacgcagcgggcgugcuuguggacugcuuggugggg
cuugcucugcuaggcggacuacuugcgugccuuguuguagacggccuugg
uaggucucuuguagaccgucgcuugcuacaauuaacgaucaacuuagaac
ugguacggacaaggggaaucugacugucuaauuaaaacauagcauugcga
uggucagaaagugauguugacgcaaugugauuucugcccagugcucugaa
ugucaaagugaagaaauucaaccaagcgcggguaaacggcguggauuaac
gagauucccacugucccuaucuacuaucuagcgaaaccacagccaaggga
acgggcuuggcagaaucagcggggaaagaagacccuguugagcuugacuc
uaguuugacauugugaagagacauagaggguguagaauaagugggagcuu
cggcgccagugaaauaccacuaccuuuauaguuucuuuacuuauucaaug
aagcggagcuggaauucauuuuccacguucuagcauucaaggucccauuc
ggggcugauccggguugaagacauugucagguggggaguuuggcuggggc
ggcacaucuguuaaacgauaacgcagauguccuaaggggggcucauggag
aacagaaaucuccaguagaacaaaaggguaaaagcccccuugauuuugau
uuucagugugaauacaaaccaugaaaguguggccuaucgauccuuuaguc
ccucggaauuugaggcuagaggugccagaaaaguuaccacagggauaacu
ggcuuguggcagucaagcguucauagcgacauugcuuuuugauucuucga
ugucggcucuuccuaucauaccgaagcagaauucgguaagcguuggauug
uucacccacuaauagggaacgugagcuggguuuagaccgucgugagacag
guuaguuuuacccuacugaugaauguuaccgcaauaguaauugaacuuag
uacgagaggaacaguucauucggauaauugguuuuugcggcugucugauc
aggcauugccgcgaagcuaccauccgcuggauuauggcugaacgccucua
agucagaauccaugcuagaacgcggugauuucuuugcuccacacaauaua
gauggauacgaauaaggcguccuuguggcgucgcugaaccauagcaggcu
agcaacggugcacuuggcggaaaggccuugggugcuugcuggcgaauugc
aaugucauuuugcguggggauaaaucauuuguauacgacuuagauguaca
acgggguauuguaagcaguagaguagccuuguuguuacgaucugcugaga
uuaagccuuuguugucugauuugu

.......................<<<<<<.....<<....>>......>>
>>>.>.........<<....>>..<<<<<......<<.....>>.....>
>>>>..<<<..<<.......<<.<<<<<<...>>>>>>.>>.......>>
....<<<<<<.<<<<<....<<<<<<<<<<<<<....<<<<......>>>
>.(.......<<<......)>>>..>.>>>>>>>>>..>>>........>
>>>>>>>>>>........<<<<<<<........>>>>>>>.....<<<<<
..((((((>>>>>..>>>................................
..<<....>>...............<<<<....>>>>.............
.....................<<<<<.<<<<<....<<<<<<<.<<<<<<
<<<<<<<<<.....<<<<<<<<<......<<<<........>>>>.....
..>>>>>>>.>.>.>>>>>.>>>>>>>>>>........<<<....>>>..
...>>>>>>>.....>>>>>.>>>>>..<<<<........>>>><<<<<<
....<<<<<<.<<<<<<..<<<...<<<<.....>>>>...>>>...<<.
...>>.......<<<<<..<<<<<....>>>>>...>>>>>.<<<<<<<<
...<<....>>...>>>.>>>.>>....>>>>>>.>>>>>>..<<.<..<
<<<<<<.....<<<<<<<<<..<<<....<<<<<<<....>>>>>>>...
..>>>...<<<..<<.<<........>>>>.>>>....>>>>>>>>>...
<<.......>>......>>>>>>...>..>.>>..<<<<<<....<.<<<
....>>>.><<<<<<<<<<...<<<.<<<<<<<.....<<<.........
..........<<<<<.....>>>>>................>>>.....>
>>>>...<<<<.<<<<.<......>>>>>.>>>>.....>>>>>.>>>>>
>>>.>>..<<<<.<<<<<.....>>>>>.>>>>....<<<......>>>.
..<<<<<<<..<<<<(((.....<<<<<<.....<<..........<<<.
<<<<<<<<<<.......<<<<<.<<<...<<.........>>...>>>..
.......<<......>>...>>>>>...>>>>>>>>>>>>>.........
.))).>>...>>>>>>.>>>>..>>>>>>><<<<<<<<<.........>>
>>>>>>>....>>>>>><.<<<<<<<<.<<......<<<<.<<<<....>
>>>>>>>...>>>>>>>>>>..>.....>>>>>><<.....<<.....<<
<<<<.......>>>>>><<<<.....<<<<<.<<...<<<<<<...<<..
...>>.>>>>>>....((<<<<<<...<<....<<<....>>>.......
..<<..............>>.....>>....>>...<<<<<........>
>>>>))<<<<.<<<<<<<.....<<<....>>>.......<<<<<<...<
<<<.<<<<<<<.<<<<<<<<<<..[[[..>>>>>><...<<<<<....<<
<<<<....<<<.....>>>....>>>>>>.....>>>>>....><<<<<<
<<....>>>>>>>>>>>>...>>>>>>>.>>>>.........>>>>>>..
........>>>..>>>>>>>>>>>>..>>.....<<......>>>>>>>.
<<<<.....>>>>..>>>>..<<<<.....<<<<<<<.<<.........<
.....<<<<<....<<..>>.....>>>>><<.<<<<<<<<.........
<<.....................<<<<<<<........<<<<.......<
.....>......>>>>........>>>>>>>...................
..<<<<<.....>>>>>.....>>..............>>..>>>>>>.>
>............<<<<<<<<<..<<<.........>>>..<<<<<<<..
..<<<<.....>>>>......>>>>>>>...<<<.<<<..<<<<<..<..
<<<.....<<<<....>>>>.....>>>>.>>>..>>>>>..>>>....>
>.>>>>>>>..>..>>.>>>>>>>..>>>>>>....>>....<<<<<...
.....>>>>>....<<<<<..<<<........<<<<<.<<<<<<..<<<<
<.<<<<<<<<..<<<<<<<<<<<<<<..<...........<<........
..................>>..>..>>>>.>>>>>>>>>>...<<<<<..
...<<<<..<<<<<......>>>>>...............<<<<<<....
>>>>>>..>>>>..>>>>>.....>>>>>>>>..>>>>>...<<<.....
>>>..<<<<<<...........>>>>>>..<<...<<<<<<<...<<<<<
<.......>>>>>>.....<<...(((>>....>>>>>>>...<<<.<<<
<<.......>>>>.>>>>.<<<....>>>.>>)))......<<<<<<<..
<<<<.))))))>>>>>>>>>>>.........>>>>..>>>>>>>......
........<<<<<....<.......>....>>>>>.............((
...<<<<.<<<<<<..<.<<<<<<<......>>>>>>>...>.<<<....
.))..>>>.....>>>>>..>...>>>>......<<<<<<<....>>>.>
>>>........>>>.>>>>>....<<<<<<<<..<<<<.<.<<<<<<...
............>>>>>>.><<<<<...<<<<....<<<<<<<<<<]]].
>>>>>..>>>>>...>>>>..>>>>>.<<<<...<<<<<...........
>>>>>...>>>>.>>>>....>>>>>>>>.......<<<<<..<<<....
...<<..........<<<<<<.....>>>>>>......>>.......<<<
<<<...<<<<<.<..<<<......>>>..>.>>>>>.>>>>>>.......
.........>>>..>>>>>..<<<<<.<.............>.....<<<
<<<<<<.<<<....<<<<.<..<<<<<......>>>>>..>>>>>...>>
>....>>>>.>>>>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8hfr Nuclear export of pre-60S particles through the nuclear pore complex.
• Resolution: 2.64 Å
• Binding residue (original residue number in PDB): G24 A50 R51 T56 F57 N95 T99 G103 F104 G105 D107 G124 D126 Y128 K142
• Binding residue (residue number reindexed from 1): G17 A43 R44 T49 F50 N88 T92 G96 F97 G98 D100 G117 D119 Y121 K135

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8hfr, PDBe:8hfr, PDBj:8hfr
• PDBsum: 8hfr
• PubMed: 37258668
• UniProt: P0C0W9|RL11A_YEAST Large ribosomal subunit protein uL5A (Gene Name=RPL11A)