Structure of PDB 6yly Chain Q Binding Site BS01

Receptor Information

>6yly Chain Q (length=134) Species: 4932 (Saccharomyces cerevisiae)

HRTAPKSDNVYLKLLVKLYTFLARRTDAPFNKVVLKALFLSKINRPPVSV
SRIARALKQEGAANKTVVVVGTVTDDARIFEFPKTTVAALRFTAGARAKI
VKAGGECITLDQLAVRAPKGQNTLILRGPRNSRE

Ligand information

>6yly Chain 1 (length=2676)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaggccagcaucag
uuuugguggcaggauaaauccauaggaauguagcuugccucgguaaguau
uauagccugugggaauacugccagcugggacugaggacugcgacguaagu
caaggaugcuggcauaaugguuauaugccgcccgucucacggaccaagga
gucuaacgucuaugcgaguguuuggguguaaaacccauacgcguaaugaa
agugaacguagguuggggccucgcaagaggugcacaaucgaccgauccug
augucuucggauggauuugaguaagagcauagcuguugggacccgaaaga
uggugaacuaugccugaauagggugaagccagaggaaacucugguggagg
cucguagcgguucugacgugcaaaucgaucgucgaauuuggguauagggg
cgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguuucccu
caggauagcagaagcucguaucaguuuuaugagaauauguaagaaguccg
acauuugaaugaagagcuuuuagugggccauuuuugguaagcagaacugg
cgaugcgggaugaaccgaacguagaguuaaggugccggaauacacgcuca
ucagacaccacaaaagguguuaguucaucuagacagccggacgguggcca
uggaagucggaauccgcuaaggaguguguaacaacucaccggccgaauga
acuagcccugaaaauggauggcgcucaagcguguuaccuauacucuaccg
ucaggguugauaugaugcccugacgaguaggcaggcguggaggucaguga
cgaagccuagaccguaaggucgggucgaacggccucuagugcagaucuug
gugguaguagcaaauauucaaaugagaacuuugaagacugaaguggggaa
agguuccacgucaacagcaguuggacguggguuagucgauccuaagagau
ggggaagcuccguuucaaaggccugacaggccaccaucgaaagggaaucc
gguuaagauuccggaaccuggauauggauucuucacgguaacguaacuga
auguggagacgucggcgcgagcccugggaggaguuaucuuuucuucuuaa
cagcuuaucaccccggaauugguuuauccggagauggggucuuauggcug
gaagaggccagcaccuuugcuggcuccggugcgcuugugacggcccguga
aaauccacaggaaggaauaguuuucaugccaggucguacugauaaccgca
gcaggucuccaaggugaacagccucuaguugauagaauaauguagauaag
ggaagucggcaaaauagauccguaacuucgggauaaggauuggcucuaag
ggucggacgaucaacuuagaacugguacggacaaggggaaucugacuguc
uaauuaaaacauagcauugcgauggucagaaagugauguugacgcaaugu
gauuuauggauuaacgagauucccacugucccuaucuacuaucuagcgaa
accacagccaaggggcuuggcagaaucagcggggacuaguuugacauugu
gaagagacauaguuucuuuacuuauucaaugaagcggagcuggaauucau
uuuccacguucuagcauucaaggucccauucggggcugauccggguugaa
gacauugucaggugguagucccucggaauuugaggcuaaacuggcuugug
gcagucaagcguucauagcgacauugcuuuuugauucuucgaugucggcu
cuuccuaucauaccgaagcagaauucgguaagcguuggauuguucaccca
cuaauagggauacccuacugaugaauguuaccgcaauaguaauugaacuu
aguacgagaggaacaguucauucggauaauugguuuuugcggcugucuga
ucaggcauugccgcgaagcuaccauccgcuggauuauggcugaacgccuc
uaagucagaauccaugcuagaacgcggugauuucuuugcuccacacaaua
uagauggauacgaauaaggcguccuuguggcgucgcugaaccauagcagg
cuagcaacggugcacuuggcggaaaggccuugggugcuugcuggcgaauu
gcaaugucauuuugcguggggauaaaucauuuguauacgacuuagaugua
caacgggguauuguaagcaguagaguagccuuguuguuacgaucugcuga
gauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6yly Construction of the Central Protuberance and L1 Stalk during 60S Subunit Biogenesis.
• Resolution: 3.8 Å
• Binding residue (original residue number in PDB): S21 K31 F35 R38 R39 L54 S55 K56 S63 S65 R66 R69 Q73 E74 K79 T86 T88 D89 D90 R92 I93 T107 A108 G134 Q135 T137 I139 L140 R141 N145 S146 R147 E148
• Binding residue (residue number reindexed from 1): S7 K17 F21 R24 R25 L40 S41 K42 S49 S51 R52 R55 Q59 E60 K65 T72 T74 D75 D76 R78 I79 T93 A94 G120 Q121 T123 I125 L126 R127 N131 S132 R133 E134

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:0043232 intracellular non-membrane-bounded organelle
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6yly, PDBe:6yly, PDBj:6yly
• PDBsum: 6yly
• PubMed: 32668200
• UniProt: P0CX49|RL18A_YEAST Large ribosomal subunit protein eL18A (Gene Name=RPL18A)