Structure of PDB 8c00 Chain Y Binding Site BS01

Receptor Information

>8c00 Chain Y (length=150) Species: 4932 (Saccharomyces cerevisiae)

GRMHSAGKGISSSAIPYSRNAPAWFKLSSESVIEQIVKYARKGLTPSQIG
VLLRDAHGVTQARVITGNKIMRILKSNGLAPEIPEDLYYLIKKAVSVRKH
LERNRKDKDAKFRLILIESRIHRLARYYRTVAVLPPNWKYESATASALVN

Ligand information

>8c00 Chain 2 (length=1425)

aucugguugauccugccaguagucauaugcuugucucaaagauuaagcca
ugcaugucuaaguauaagcaaauacagugaaacugcgaauggcucauuaa
aucaguuaucguuuauuugauaguuacaugguauaacugugguaauucua
gagcuaauacaugcuuaaaaucucgaagagauguauuuauuagauaaaaa
auugaugauucauaauaacuuuucgaaucgcauggccgcuggcgaugguu
cauucaaauuucugcccuaucaacuuucgaugguaggauaguggccuacc
augguuucaacggguaacggggaauaaggguucgauuccggagagggagc
cugagaaacggcuaccacauccaaggaaggcagcaggcgcgcaaauuacc
caauccuaauucagggagguagugacaauaaauaacgauacagguuguau
uggaaugaguacaauguaaauaccuuaacgaggaacaauuggagggcaag
ucuggugagcagccgcggauuccagcuccaauagcguauauuaaaguugu
ugcaguuaaaaagcucguaguugaacuuugggcccgguuggccaacgggg
ccuuuuuuacuuugaaaaaauuagaguguucaaagcaggcgugcucgaau
auauuagcauggaauaauagaauaggacguuugguucuauuuuuuucuag
gaccaucguaaugauuaauagggacggucgggggcaucaguauucaauug
ucagaggugaaauucuuggauuuauugaagacuaacuacugcgaaagcau
uugccaaggacguuuucauuaaucaagaacgaaaguuaggggaucgaaga
ugaucagauaccgucguagucuuaaccauaaacuaugccgacuagggauc
gggugguguuuuuaaugacccacucggcaccuuacgagaaaucaaagucu
uuggguucuggggggaguauggucgcaaggcugaaacuuaaaggaauuga
agggcaccaccaggaguggagccugcggcuuaauuugaaacucaccaggu
ccacacaauaagauugacagauugagagcuuucuugauuugugguagugg
ugcuagcaugcuggucacuguucugggcgcacgcgcgcuacacugacgga
gccagcgagucuaaccuuggccgagaggucuugguaaucuugugaaacuc
cgucgugcuggggauagagcauuguaauuauugcucuucaacgaggaauu
ccuaguaagcgcaagucaucagcuugcguugauuacgucccugcccugua
ccuaguaccgauugaauggcuuagugaggccucaggaucugcuuagaguc
agagcggagaauuuggacaaacuuggucauuuagaggaacuagguuuccg
uaggugaaccugcggaaggaucauu

..<<<<<.[[((((>>>>><<<<.<<<<<<...<.<...<......<<<.
<<<..<<....<<....<<.......>>...>>.>>......<<......
..<<<..<<..<<....<<<........<<......<<.<<<.....>>>
.>>......>>........<<<<<...>>>>><.<.<<<<<<......((
(...........>>>>>>.>...>...<<<<..<<<.>>>.>>>>....>
>>...>>>>..>>>.<<<....<<<....<<<<<<<<.......>>>>>>
>>>>>......>>>...<<<.<<<<....>>>>....>>>.>>.<<.<<<
..........>>>.>>.<.<<....>>.>...>>>>>>.........<<<
....<<<.....>>>..>>>..>....>.>.....<<<<<<<<.>>>>>>
>>......<<..<...........>..>>.........<<<<<((....<
.<<<<...<<..))>>.....>>>>>>>>>>..>>>>>>>>>>.......
..<<<[[.....<.<<...<<<.<<....<<<<<<.<<<<..>>>>.>>>
>>>...<<<<<.<<.......<<...<.......>..<<<..>>>....>
>......>>.>>..>>>.........<<<..<<<<<<<<....))).>>>
>>>>>.>>>.....>>....<<<<<<.<<...<<<<..<<..<<<<<<.<
...<<<..(...>>>......>.>>>>>>..>>.......<<....>>..
.>>>>...>>>>>.>>>...>>>...>>.>....<<<<<<<...<...<<
<<..)......>>>>...>>>>>>>>..........<<<.<<.<<<..<<
<<<<<<.<<<......>>>>>>>>>>>..>>>...<<..]]>>...>>..
...>>>.>>>.<<<......<<<<....>>>>....>>>..)))).]]..
<<<<<<..<<..<<<<<..<<<.<<<<<<...............<<<<<.
<..<<<<<.......<<.<<........>>.>>.....>>>>>..<<<<.
.<<<<<<..>>>>>>>>>>>.>>>>>..>>.>>>>.>>>.....<<<<<<
<......<<.....<<..<<<<....>>>>..>>....>>.......>>>
>>>>......<....<<<<<<..........>>>>>>....>.....>>>
>>.....<<<<<<<<.......>>>>>>>>......>>...>>>>>>...
..<<<..<<....<<<<<<<<.<<<..<.<<..<...<<<<<<.......
..>>>>>>...>..>>.>..>>>.>>>>>>>>...>>..>>>...<<<<<
<<<<....>>>>>>>>>........

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8c00 Impact of the yeast S0/uS2-cluster ribosomal protein rpS21/eS21 on rRNA folding and the architecture of small ribosomal subunit precursors.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): G2 R3 G8 G10 I11 S12 S14 P17 R20 S48 G51 R55 R64 K70 M72 R73 D87 Y90 H101 N105 K107 D108 F113 R114 R121 R124 R127 Y128
• Binding residue (residue number reindexed from 1): G1 R2 G7 G9 I10 S11 S13 P16 R19 S47 G50 R54 R63 K69 M71 R72 D86 Y89 H100 N104 K106 D107 F112 R113 R120 R123 R126 Y127

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0070181 small ribosomal subunit rRNA binding

Biological Process

• GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0030686 90S preribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8c00, PDBe:8c00, PDBj:8c00
• PDBsum: 8c00
• PubMed: 36996028
• UniProt: P05756|RS13_YEAST Small ribosomal subunit protein uS15 (Gene Name=RPS13)