Structure of PDB 8v83 Chain Y Binding Site BS01

Receptor Information

>8v83 Chain Y (length=125) Species: 1247190 (Saccharomyces cerevisiae BY4741)

AKQSLDVSSDRRKARKAYFTAPSSQRRVLLSAPLSKELRAQYGIKALPIR
RDDEVLVVRGSKKGQEGKISSVYRLKFAVQVDKVTKEKVNGASVPINLHP
SKLVITKLHLDKDRKALIQRKGGKL

Ligand information

>8v83 Chain 1 (length=2015)

guuugaccucaaaucagguaggaguacccgcugaacaauaagcggaggaa
aagaaaccaaccgggauugccuuaguaacggcgagugaagcggcaaaagc
ucaaauuugaaaucugguaccuucggugcccgaguuguaauuuggagagg
gcaacuuuggggccguuccuugucuauguuccuuggaacaggacgucaua
gagggugagaaucccguguggcgaggagugcgguucuuuguaaagugccu
ucgaagagucgaguuguaugcagcucuaagugggugguaaauuccaucua
aagcuaaauauuggcgagagaccgauagcgaacaaguacagugauggaaa
gaugaaaagaacuuugaaaagagagugaaaaaguacgugaaauuguugaa
agggaagggcauuugaucagacaugguguuuugugcccucugcuccuugu
ggguaggggaaucucgcauuucacugggccagcaucaguuuugguggcag
gauaaauccauaggaauguagcuugccucgguaaguauuauagccugugg
gaauacugccagcugggacugaggacugcgacguaagucaaggaugcugg
cauaaugguuauaugccgcccgucuugaaacacggaccaaggagucuaac
gucuaugcgaguguuuggguguaaaacccauacgcguaaugaaagugaac
guagguuggggccucgcaagaggugcacaaucgaccgauccugaggaugg
auuugaguaagagcauagcuguugggacccgaaagauggugaacuaugcc
ugaaggguauaggggcaagacaccaucuaguagcugguuccugccgaagu
uucccucaggauagcagaagcucguaucaguuuuagaaugaagagcuuuu
agugggccauuuuugguaagcagaacuggcgaugcgggaugaaccgaacg
uagaguuaaggugccggaauacacgcucaucagacaccacaaaagguguu
aguucaucuagacagccggacgguggccauggaagucggaauccgcuaag
gaguguguaacaacucaccggccgaaugaacuagcccugaaaauggaugg
cgcucaagcguguuaccuauacucuaccgucaggguugauaugaugcccu
gacgaguaggcaggcguggaggucagugacgaagccuagaccguaagguc
gggucgaacggccucuagugcagaucuuggugguaguagcaaauauucaa
augaggaacagccucuaguugauagaauaauguagauauaucuacuaucu
agcgaaaccacagccaagggaacgggcuuggcagaaucagcggggaaaga
agacccuguugagcuugacucuaguuugacauugugaagagacauagagg
guguagaauaagugggagcuucggcgccagugaaauaccacuaccuuuau
aguuucuuuacuauugucagguggggaguaaaguuaccacagggauaacu
ggcuuguggcagucaagcguucauagcgacauugcuugauucucggcucu
uccuaucauaccgaagcagaauucgguaagcguuggauuguucaccggga
acgugagcugggucgucgugagacaggccuacugaguuaccgcaauagua
auugaacuuaguacgagaggaacaguucauucggauaauugguuuugcgg
cugucugaucaggcauugccgcgaagcuaccauccgcuggauuauggcug
aacgccucuaagucagaauccaugcuagaacgcggugaugcuccacacag
auggauacgaauaaggcguccuuguggcgucgcugaaccauagcaggcua
gcaacggugcacuuggcggaaaggccuugggugcuugcuggcgaauugca
augcguggggauaaaucauuuguauacgacuuagauguacaacgggguau
uguaagcaguagaguagccuuguuguuacgaucugcugagauuaagccuu
uguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8v83 The DEAD-box ATPase Dbp10/DDX54 initiates peptidyl transferase center formation during 60S ribosome biogenesis.
• Resolution: 2.53 Å
• Binding residue (original residue number in PDB): A2 K3 Q4 S5 S9 S10 R12 K14 A15 R16 Y19 V29 L30 S32 P34 K37 R40 K46 R60 G61 S62 K87 K89 V90 N91 H100 S102 K103 R121 K122
• Binding residue (residue number reindexed from 1): A1 K2 Q3 S4 S8 S9 R11 K13 A14 R15 Y18 V28 L29 S31 P33 K36 R39 K45 R59 G60 S61 K86 K88 V89 N90 H99 S101 K102 R120 K121

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• 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:8v83, PDBe:8v83, PDBj:8v83
• PDBsum: 8v83
• PubMed: 38632236
• UniProt: P05743|RL26A_YEAST Large ribosomal subunit protein uL24A (Gene Name=RPL26A)