Structure of PDB 8v84 Chain m Binding Site BS01

Receptor Information

>8v84 Chain m (length=211) Species: 1247190 (Saccharomyces cerevisiae BY4741)

YSKYADGSDRIIKPEINPVYDSDDSDAETQNTIGNIPLSAYDEMPHIGYD
INGKRIMRPNPYEPLIDWFTRHEEVMPLTAVPEPKRRFVPSKNEAKRVMK
IVRAIREGRIIPPKKLKEMKEKEKIENYQYDLWGHLRAPKLPPPTNEESY
NPPEEYLLSPEEKEAWENTEYSERERNFIPQKYSALRKVPGYGESIRERF
ERSLDLYLAPR

Ligand information

>8v84 Chain 1 (length=1970)

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
ggcuuguggcagucaagcguucauagcgacauugcuugauucuauaccga
agcagaauucgguaagccgucgugagacaggccuacugaguuaccgcaau
aguaauugaacuuaguacgagaggaacaguucauucggauaauugguuuu
ugcggcugucugaucaggcauugccgcgaagcuaccauccgcuggauuau
ggcugaacgccucuaagucagaauccaugcuagaacgcggugaugcucca
cacagauggauacgaauaaggcguccuuguggcgucgcugaaccauagca
ggcuagcaacggugcacuuggcggaaaggccuugggugcuugcuggcgaa
uugcaaugcguggggauaaaucauuuguauacgacuuagauguacaacgg
gguauuguaagcaguagaguagccuuguuguuacgaucugcugagauuaa
gccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8v84 The DEAD-box ATPase Dbp10/DDX54 initiates peptidyl transferase center formation during 60S ribosome biogenesis.
• Resolution: 2.7 Å
• Binding residue (original residue number in PDB): V259 K263 R264 R265 V267 P268 S269 E272 R275 M277 R281 R287 I288
• Binding residue (residue number reindexed from 1): V81 K85 R86 R87 V89 P90 S91 E94 R97 M99 R103 R109 I110

Gene Ontology

Molecular Function

• GO:0003674 molecular_function
• GO:0003677 DNA binding
• GO:0005515 protein binding
• GO:0043021 ribonucleoprotein complex binding
• GO:0070180 large ribosomal subunit rRNA binding

Biological Process

• 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:8v84, PDBe:8v84, PDBj:8v84
• PDBsum: 8v84
• PubMed: 38632236
• UniProt: Q04660|ERB1_YEAST Ribosome biogenesis protein ERB1 (Gene Name=ERB1)