Structure of PDB 8v83 Chain a Binding Site BS01

Receptor Information

>8v83 Chain a (length=210) Species: 1247190 (Saccharomyces cerevisiae BY4741)

QVREHVKELLKYSNETKKRNFLETVELQVGLKNYDPQRDKRFSGSLKLPN
CPRPNMSICIFGDAFDVDRAKSCGVDAMSVDDLKKLNKNKKLIKKLSKKY
NAFIASEVLIKQVPRLLGPQLSKAGKFPTPVSHNDDLYGKVTDVRSTIKF
QLKKVLCLAVAVGNVEMEEDVLVNQILMSVNFFVSLLKKNWQNVGSLVVK
SSMGPAFRLY

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): R26 N27 F28 E33 R60 K101 K105 L163 C164 A166 K207 S209 M210 G211 A213 R215
• Binding residue (residue number reindexed from 1): R19 N20 F21 E26 R53 K94 K98 L156 C157 A159 K200 S202 M203 G204 A206 R208

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000055 ribosomal large subunit export from nucleus
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042254 ribosome biogenesis

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8v83, PDBe:8v83, PDBj:8v83
• PDBsum: 8v83
• PubMed: 38632236
• UniProt: P0CX43|RL1A_YEAST Large ribosomal subunit protein uL1A (Gene Name=RPL1A)