Structure of PDB 6ylx Chain M Binding Site BS01

Receptor Information

>6ylx Chain M (length=137) Species: 4932 (Saccharomyces cerevisiae)

STDSIVKASNWRLVEVGRVVLIKKGQSAGKLAAIVEIIDQKKVLIDGPKA
GVPRQAINLGQVVLTPLTFALPRGARTATVSKKWAAAAVCEKWAASSWAK
KIAQRERRAALTDFERFQVMVLRKQKRYTVKKALAKA

Ligand information

>6ylx Chain 1 (length=2534)

guuugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaau
aagcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaa
gcggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguugua
auuuggagagggcaacuuuggggccguuccuugucuauguuccuuggaac
aggacgucauagagggugagaaucccguguggcgaggagugcgguucuuu
guaaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugg
gugguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaac
aaguacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaag
uacgugaaauuguugaaagggaagggcauuugaucagacaggccagcauc
aguuuugguggcaggauaaauccauaggaauguagcuugccucgguaagu
auuauagccugugggaauacugccagcugggacugaggacugcgacguaa
gucaaggaugcuggcauaaugguuauaugccgcccgucuugaaacacgga
ccaaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcg
uaaugaaagugaacguagguuggggccucgcaagaggugcacaaucgacc
gauccugaugucuucggauggauuugaguaagagcauagcuguugggacc
cgaaagauggugaacuaugccugaauagggugaagccagaggaaacucug
guggaggcucguagcgguucugacgugcaaaucgaucgucgaauuugggu
auaggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaag
uuucccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaa
aacuuuaaauauguaagaagucggacauuugaaugaagagcuuuuagugg
gccauuuuugguaagcagaacuggcgaugcgggaugaaccgaacguagag
uuaaggugccggaauacacgcucaucagacaccacaaaagguguuaguuc
aucuagacagccggacgguggccauggaagucggaauccgcuaaggagug
uguaacaacucaccggccgaaugaacuagcccugaaaauggauggcgcuc
aagcguguuaccuauacucuaccgucaggguugauaugaugcccugacga
guaggcaggcguggaggucagugacgaagccuagaccguaaggucggguc
gaacggccucuagugcagaucuuggugguaguagcaaauauucaaaugag
aacuuugaagacugaaguggggaaagguuccacgucaacagcaguuggac
guggguuagucgauccuaagagauggggaagcuccguuucaaaggccuga
uuuuaugcaggccaccaucgaaagggaauccgguuaagauuccggaaccu
ggauauggauucuucacgguaacguaacugaauguggagacgucggcgcg
agcccugggaggaguuaucuuuucuucuuaacagcuuaucaccccggaau
ugguuuauccggagauggggucuuauggcuggaagaggccagcaccuuug
cuggcuccggugcgcuugugacggcccgugaaaauccacaggaaggaaua
guuuucaugccaggucguacugauaaccgcagcaggucuccaaggugaac
agccucuaguugauagaauaauguagauaagggaagucggcaaaauagau
ccguaacuucgggauaaggauuggcucuaagggucggacgaucaacuuag
aacugguacggacaaggggaaucugacugucuaauuaaaacauagcauug
auuuauggauuaacgagauucccacugucccuaucuacuaucuagcgaaa
ccacagccaagggggcuuggcagaaucagcggggaaacuggcuuguggca
gucaagcguucauagcgacauugcuuuuugauucuucgaugucggcucuu
ccuaucauaccgaagcagaauucgguaagcguuggauuguucacccacua
auagggagugagcuggguuacccuacugaugaauguuaccgcaauaguaa
uugaacuuaguacgagaggaacaguucauucggauaauugguuuuugcgg
cugucugaucaggcauugccgcgaagcuaccauccgcuggauuauggcug
aacgccucuaagucagaauccaugcuagaacgcggugauuucuuugcucc
acacaauauagauggauacgaauaaggcguccuuguggcgucgcugaacc
auagcaggcuagcaacggugcacuuggcggaaaggccuugggugcuugcu
ggcgaauugcaaugucauuuugcguggggauaaaucauuuguauacgacu
uagauguacaacgggguauuguaagcaguagaguagccuuguuguuacga
ucugcugagauuaagccuuuguugucugauuugu

...........................<<<<<.....<<....>>.....
.>>>>>.....<.....<<....>>..<<<<<......<<.....>>...
..>>>>>..<<<...........<<.<<<<<<...>>>>>>.>>......
.......<<<<<<.<<<<<<<<<<<<<<<<<<<<<.....<<<<......
>>>>.(.......<<<......)>>>....>>>>>>>>..>>>>>>>>..
..>>>>>>>>>>>........<<<<<<<........>>>>>>>.....<<
<<<........>>>>>..>>>....>........................
.....<<....>>...............<<<<....>>>>..........
........................<<<<<.<<<<<......<<<<<<<.<
<<<<<<<<<<<<<<.....<<<<<<<<<......<<<<<......>>>>>
.......>>>>>>>.>.>.>>>>>.>>>>>>>>>>........<<<....
>>>.....>>>>>>>.....>>>>>.>>>>>..<<<<........>>>><
<<<<<....<<<<<<.<<<<<<..<<<...<<<<.....>>>>...>>>.
..<<....>>.......<<<<<..<<<<<....>>>>>...>>>>>.<<<
<<<<<...<<....>>...>>>.>>>.>>....>>>>>>.>>>>>>..<<
.<...<<<<<<.....<<<<<<<<<..<<<....<<<<<<<....>>>>>
>>.....>>>...<<<..<<.<<........>>>>.>>>....>>>>>>>
>>...<<.......>>......>>>>>>......>.>>..<<<<<<....
<.<<<....>>>.><<<<<<<<.....<<<.<<<<<<.............
............>>>>...<<<.>>>.....>>>>>...>>>>>>.>>..
<<<<.<<<<<.....>>>>>.>>>>....<<<......>>>...<<<<<<
<..<<<<(((.....<<<<<<......<..........<<<.<<<<<<<<
<<.......<<<<<.<<....<<.........>>....>>.........<
<......>>...>>>>>...>>>>>>>>>>>>>..........))).>..
..>>>>>>.>>>>..>>>>>>><<<<<<<<<.........>>>>>>>>>.
...>>>>>><<.<<<<<<..<<......<<<<.<<<<....>>>>>>>>.
..>>.>>>>>>..>>.....>>>>>><<.....<<.....<<<<<<....
...>>>>>><<<<.....<<<<<.<<...<<<<<<...<<.....>>.>>
>>>>....((<<<<<<...<<....<<<....>>>........<<<<<<.
.......>>>>>>....>>....>>...<<<<<........>>>>>))<<
<<.<<<<<<<.....<<<....>>>.......<<<<<<...<<<<.<<<<
<<<<<<<<<<<<<<..(((..>>>>>><...<<<<<....<<<<<<....
<<<.....>>>....>>>>>>.....>>>>>....><<<<<<<<....>>
>>>>>>>>>>.>.>>>>>>>.>>>>.........>>>>>>..........
>>>..>>>>>>>>>>>>..>>.....<<......>>>>>>>.<<<<....
.>>>>..>>>>..<<<<.....<<<<<<<.<<...............<<<
<<...............>>>>><<.<<<<<<<<<<....>>>>..>>>>>
>.>>............<<<<<<<....<<<.........>>>..<...>.
................>>>>>>>.....>>.>>>>>>>..>>>>>>....
>>....<<<<<....>>>>>....<<<<<..<<.............<<<<
<<...<<.......>>...>>>>>>......................<<<
<<<..<.<<<<<<<......>>>>>>>...>.<<<.........>>>...
..>>>>>>..............>>.>>>>>....<<<<<<<<..<<<<.<
.<<<<<<...............>>>>>>.><<<<<....<<<...<<<<<
<<<<<<))).>>>>>..>>>>>>..>>>...>>>>>.<<<<...<<<<<.
..........>>>>>...>>>>.>>>>....>>>>>>>>.......<<<<
<<.<<<.<<....<<..........<<<<<<.....>>>>>>......>>
.......<<<<<<...<<<<<.<..<<<......>>>..>.>>>>>.>>>
>>>.............>>.>>>.>>>>>>..<<<<<.<............
.>.....<<<<<<<<<.<<<....<<<<....<<<<........>>>>..
.>>>>...>>>....>>>>.>>>>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6ylx Construction of the Central Protuberance and L1 Stalk during 60S Subunit Biogenesis.
• Resolution: 3.9 Å
• Binding residue (original residue number in PDB): I6 R13 N59 R74 G75 A76 R77 T78 T80 K83 K84 S98 W99 R106 R109 F118 M121 V122 R124 K125 Q126 R128 Y129 K132 K133 A136
• Binding residue (residue number reindexed from 1): I5 R12 N58 R73 G74 A75 R76 T77 T79 K82 K83 S97 W98 R105 R108 F117 M120 V121 R123 K124 Q125 R127 Y128 K131 K132 A135

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0000470 maturation of LSU-rRNA
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0016236 macroautophagy
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• 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:6ylx, PDBe:6ylx, PDBj:6ylx
• PDBsum: 6ylx
• PubMed: 32668200
• UniProt: P36105|RL14A_YEAST Large ribosomal subunit protein eL14A (Gene Name=RPL14A)