Structure of PDB 6oig Chain O Binding Site BS01

Receptor Information

>6oig Chain O (length=197) Species: 4932 (Saccharomyces cerevisiae)

VEPVVVIDGKGHLVGRLASVVAKQLLNGQKIVVVRAEELNISGEFFRNKL
KYHDFLRKATAFNKTRGPFHFRAPSRIFYKALRGMVSHKTARGKAALERL
KVFEGIPPPYDKKKRVVVPQALRVLRLKPGRKYTTLGKLSTSVGWKYEDV
VAKLEAKRKVSSAEYYAKKRAFTKKVASANATAAESDVAKQLAALGY

Ligand information

>6oig Chain 5 (length=3243)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaugguguuuugua
uuucacuggccagcaucaguuuugguggcaggauaaauccauaggaaugu
agcuugccucgguaaguauuauagccugugggaauacugccagcugggac
ugaggacugcgacguaagucaaggaugcuggcauaaugguuauaugccgc
ccgucuugaaacacggaccaaggagucuaacgucuaugcgaguguuuggg
uguaaaacccauacgcguaaugaaagugaacguagguuggggccucgcaa
gaggugcacaaucgaccgauccugaugucuucggauggauuugaguaaga
gcauagcuguugggacccgaaagauggugaacuaugccugaauaggguga
agccagaggaaacucugguggaggcucguagcgguucugacgugcaaauc
gaucgucgaauuuggguauaggggcgaaagacuaaucgaaccaucuagua
gcugguuccugccgaaguuucccucaggauagcagaagcucguaucaguu
uuaugagguaaagcgaaugauuagagguuccggggucgaaaugaccuuga
ccuauucucaaacuuuaaauauguaagaaguccuuguuacuuaauugaac
guggacauuugaaugaagagcuuuuagugggccauuuuugguaagcagaa
cuggcgaugcgggaugaaccgaacguagaguuaaggugccggaauacacg
cucaucagacaccacaaaagguguuaguucaucuagacagccggacggug
gccauggaagucggaauccgcuaaggaguguguaacaacucaccggccga
augaacuagcccugaaaauggauggcgcucaagcguguuaccuauacucu
accgucaggguugauaugaugcccugacgaguaggcaggcguggagguca
gugacgaagccuagaccguaaggucgggucgaacggccucuagugcagau
cuuggugguaguagcaaauauucaaaugagaacuuugaagacugaagugg
ggaaagguuccacgucaacagcaguuggacguggguuagucgauccuaag
agauggggaagcuccguuucaaaggccugauuuuaugcaggccaccaucg
aaagggaauccgguuaagauuccggaaccuggauauggauucuucacggu
aacguaacugaauguggagacgucggcgcgagcccugggaggaguuaucu
uuucuucuuaacagcuuaucaccccggaauugguuuauccggagaugggg
ucuuauggcuggaagaggccagcaccuuugcuggcuccggugcgcuugug
acggcccgugaaaauccacaggaaggaauaguuuucaugccaggucguac
ugauaaccgcagcaggucuccaaggugaacagccucuaguugauagaaua
auguagauaagggaagucggcaaaauagauccguaacuucgggauaagga
uuggcucuaagggucggguagugagggucgcuugcuacaacgaucaacuu
agaacugguacggacaaggggaaucugacugucuaauuaaaacauagcau
ugcgauggucagaaagugauguugacgcaaugugauuucugcccagugcu
cugaaugucaaagugaagaaauucaaccaagcgcggguaaacggcgggag
uaacuaugacucucuuaagguagccaaaugccucgucaucuaauuaguga
cgcgcaugaauggauuaacgagauucccacugucccuaucuacuaucuag
cgaaaccacagccaagggaacgggcuuggcagaaucagcggggaaagaag
acccuguugagcuugacucuaguuugacauugugaagagacauagagggu
guagaauaagugggagcuucggcgccagugaaauaccacuaccuuuauag
uuucuuuacuuauucaaugaagcggagcuggaauucauuuuccacguucu
agcauucaaggucccauucggggcugauccggguugaagacauugucagg
uggggaguuuggcuggggcggcacaucuguuaaacgauaacgcagauguc
cuaaggggggcucauggagaacagaaaucuccaguagaacaaaaggguaa
aagcccccuugauuuugauuuucagugugaauacaaaccaugaaagugug
gccuaucgauccuuuagucccucggaauuugaggcuagaggugccagaaa
aguuaccacagggauaacuggcuuguggcagucaagcguucauagcgaca
uugcuuuuugauucuucgaugucggcucuuccuaucauaccgaagcagaa
uucgguaagcguuggauuguucacccacuaauagggaacgugagcugggu
uuagaccgucgugagacagguuaguuuuacccuacugaugaauguuaccg
caauaguaauugaacuuaguacgagaggaacaguucauucggauaauugg
uuuuugcggcugucugaucaggcauugccgcgaagcuaccauccgcugga
uuauggcugaacgccucuaagucagaauccaugcuagaacgcggugauuu
cuuugcuccacacaauauagauggauacgaauaaggcguccuuguggcgu
cgcugaaccauagcaggcuagcaacggugcacuuggcggaaaggccuugg
gugcuugcuggcgaauugcaaugucauuuugcguggggauaaaucauuug
uauacgacuuagauguacaacgggguauuguaagcaguagaguagccuug
uuguuacgaucugcugagauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6oig An open interface in the pre-80S ribosome coordinated by ribosome assembly factors Tsr1 and Dim1 enables temporal regulation of Fap7.
• Resolution: 3.8 Å
• Binding residue (original residue number in PDB): P5 G17 R18 S21 V22 K25 K32 S44 E46 F48 R49 R59 K60 A61 F64 T67 R68 H72 F73 R74 K82 A83 R85 G86 M87 H90 K91 R94 R101 I108 P109 P110 D113 K114 K115 K116 R117 Q122 R128 L129 K130 R133 V145 Y149 V153 L156 E157 K161 S164 A165 Y167 Y168 K171 R172 K176
• Binding residue (residue number reindexed from 1): P3 G15 R16 S19 V20 K23 K30 S42 E44 F46 R47 R57 K58 A59 F62 T65 R66 H70 F71 R72 K80 A81 R83 G84 M85 H88 K89 R92 R99 I106 P107 P108 D111 K112 K113 K114 R115 Q120 R126 L127 K128 R131 V143 Y147 V151 L154 E155 K159 S162 A163 Y165 Y166 K169 R170 K174

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0000470 maturation of LSU-rRNA
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0017148 negative regulation of translation

Cellular Component

• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6oig, PDBe:6oig, PDBj:6oig
• PDBsum: 6oig
• PubMed: 33219089
• UniProt: P26784|RL16A_YEAST Large ribosomal subunit protein uL13A (Gene Name=RPL16A)