Structure of PDB 6ylx Chain n Binding Site BS01

Receptor Information

>6ylx Chain n (length=371) Species: 4932 (Saccharomyces cerevisiae)

MRIKKKNTRGNARNFITRSQAVRKLQVSLADFRRLCIFKGIYPREPRNKK
KANKGSTAPTTFYYAKDIQYLMHEPVLAKFREHKTFARKLTRALGRGEVS
SAKRLEENRDSYTLDHIIKERYPSFPDAIRDIDDALNMLFLFSNLPSTNQ
VSSKIINDAQKICNQWLAYVAKERLVRKVFVSIKGVYYQANIKGEEVRWL
VPFKFPENIPSDVDFRIMLTFLEFYSTLLHFVLYKLYTDSGLIYPPKLDL
KKDKIISGLSSYILESRKYDSPVASLFSAFVFYVSREVPIDILEFLILSC
GGNVISEAAMDQIDMSKVTHQIVDRPVLKNKVAGRTYIQPQWIFDCINKG
ELVPANKYLPGEALPPHLSPW

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): M1 R2 I3 K6 N11 S19 Q20 R23 S28 L29 R33 R34 R47 K50 K51 S56 T57 H83 K84 A87 K89 T91 R92 R96 R104 N149 Q150 D214 R216
• Binding residue (residue number reindexed from 1): M1 R2 I3 K6 N11 S19 Q20 R23 S28 L29 R33 R34 R47 K50 K51 S56 T57 H83 K84 A87 K89 T91 R92 R96 R104 N149 Q150 D214 R216

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003729 mRNA binding
• GO:0005515 protein binding
• GO:0043021 ribonucleoprotein complex binding
• GO:0070180 large ribosomal subunit rRNA binding

Biological Process

• GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0000466 maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0006364 rRNA processing
• GO:0042254 ribosome biogenesis
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0030687 preribosome, large subunit precursor
• GO:0070545 PeBoW complex

External links

• PDB: RCSB:6ylx, PDBe:6ylx, PDBj:6ylx
• PDBsum: 6ylx
• PubMed: 32668200
• UniProt: P53261|PESC_YEAST Pescadillo homolog (Gene Name=NOP7)