Structure of PDB 6ylg Chain j Binding Site BS01

Receptor Information

>6ylg Chain j (length=84) Species: 4932 (Saccharomyces cerevisiae)

GKGTPSFGKRHNKSHTLCNRCGRRSFHVQKKTCSSCGYPAAKTRSYNWGA
KAKRRHTTGTGRMRYLKHVSRRFKNGFQTGSASK

Ligand information

>6ylg Chain 1 (length=3039)

guuugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaau
aagcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaa
gcggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguugua
auuuggagagggcaacuuuggggccguuccuugucuauguuccuuggaac
aggacgucauagagggugagaaucccguguggcgaggagugcgguucuuu
guaaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugg
gugguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaac
aaguacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaag
uacgugaaauuguugaaagggaagggcauuugaucagagccagcaucagu
uuugguggcaggauaaauccauaggaauguagcuugccucgguaaguauu
auagccugugggaauacugccagcugggacugaggacugcgacguaaguc
aaggaugcuggcauaaugguuauaugccgcccgucuugaaacacggacca
aggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcguaa
ugaaagugaacguagguuggggccucgcaagaggugcacaaucgaccgau
ccugaugucuucggauggauuugaguaagagcauagcuguugggacccga
aagauggugaacuaugccugaauagggugaagccagaggaaacucuggug
gaggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguaua
ggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguuu
cccucaggauagcagaagcucguaucaguuuuaugagauuagagguuccg
gggucgaaaugaccuugaccuauucuguaagaaguccuuguuugaacgug
gacgaaugaagcuuuuagugggccauuuuugguaagcagaacuggcgaug
cgggaugaaccgaacguagaguuaaggugccggaauacacgcucaucaga
caccacaaaagguguuaguucaucuagacagccggacgguggccauggaa
gucggaauccgcuaaggaguguguaacaacucaccggccgaaugaacuag
cccugaaaauggauggcgcucaagcguguuaccuauacucuaccgucagg
guuaugcccugacgaguaggcaggcguggaggucagugacgaagccuaga
ccguaaggucgggucgaacggccucuagugcagaucuuggugguaguagc
aaauauucaaaugagaacuuugaagacugaaguggggaaagguuccacgu
caacagcaguuggacguggguuagucgauccuaagagauggggaagcucc
guuucaaaggccuggcaggccaccaucgaaagggaauccgguuaagauuc
cggaaccuggauauggauucuucacgguaacguaacugaauguggagacg
ucggcgcgagcccugggaggaguuaucuuuucuucuuaacagcuuaucac
cccggaauugguuuauccggagauggggucuuauggcuggaagaggccag
caccuuugcuggcuccggugcgcuugugacggcccgugaaaauccacagg
aaggaauaguuuucaugccaggucguacugauaaccgcagcaggucucca
aggugaacagccucuaguugauagaauaauguagauaagggaagucggca
aaauagauccguaacuucgggauaaggauuggcucuaagggucggcgauc
aacuuagaacugguacggacaaggggaaucugacugucuaauuaaaacau
agcauugcgauggucagaaagugauguugacgcaaugugauuucugccca
gugcucugaaugucaaagugaagaaauucaaccaagcgcggguaaacggc
gggaguacucucuuaagguagggauuaacgagauucccacugucccuauc
uacuaucuagcgaaaccacagccaagggaacgggcuuggcagaaucagcg
gggaaagacccuguugagcuugacucuaguuugacauugugaagagacau
agaggguguagaauaagugggagcuucggcgccagugaaauaccacuacc
uuuauaguuucuuuacuuauucaaugaagcggagcuggaauucauuuucc
acguucuagcauucaaggucccauucggggcugauccggguugaagacau
ugucagguggggaguuucacaucuguugcagaugucuaaggggggcucau
ggagaacagaaaucuccaguagaacaaaggguaaaagcccccuugauuuu
gauuuuugugaauacaaaccaugaaaguguggccccuuuagucccucgga
auuugaggcuagaggaaaguuaccacaggguggcuuguggcagucaagcg
uucauagcgacauugcuuuuugauucuucgaucggcucuuccuaucauac
cgaagcagaauucgguaagcguuggauuguucacccacuaauagggaacg
ugagcugguagaccgucgugagacagguuaguuuuacccuacugaugaau
guuaccgcaauaguaauugaacuuaguacgagaggaacaguucauucgga
uaauugguuuuugcggcugucugaucaggcauugccgcgaagcuaccauc
cgcuggauuauggcugaacgccucuaagucagaauccaugcuagaacgcg
gugauuugcuccacacaaauagauggauacgaauaaggcguccuuguggc
gucgcugaaccauagcaggcuagcaacggugcacuuggcggaaaggccuu
gggugcuugcuggcgaauugcaaugucauuugcguggggauaaaucauuu
guauacgacuuagauguacaacgggguauuguaagcaguagaguagccgu
uacgaucugcugagauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6ylg Construction of the Central Protuberance and L1 Stalk during 60S Subunit Biogenesis.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): G2 K3 T5 P6 S7 F8 G9 K10 R11 H12 N13 K14 S15 H16 R24 R25 S26 H28 Q30 K31 S35 K43 T44 R45 Y47 N48 W49 K52 R55 R56
• Binding residue (residue number reindexed from 1): G1 K2 T4 P5 S6 F7 G8 K9 R10 H11 N12 K13 S14 H15 R23 R24 S25 H27 Q29 K30 S34 K42 T43 R44 Y46 N47 W48 K51 R54 R55

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0008270 zinc ion binding
• GO:0019843 rRNA binding
• GO:0046872 metal ion binding

Biological Process

• GO:0000448 cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• 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:0030687 preribosome, large subunit precursor
• GO:0044391 ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6ylg, PDBe:6ylg, PDBj:6ylg
• PDBsum: 6ylg
• PubMed: 32668200
• UniProt: P49166|RL37A_YEAST Large ribosomal subunit protein eL37A (Gene Name=RPL37A)