Structure of PDB 8v84 Chain D Binding Site BS01

Receptor Information

>8v84 Chain D (length=423) Species: 1247190 (Saccharomyces cerevisiae BY4741)

VEKFEELKLSQPTLKAIEKMGFTTMTSVQARTIPPLLAGRDVLGAAKTGS
GKTLAFLIPAIELLHSLKFKPRNGTGIIVITPTRELALQIFGVARELMEF
HSQTFGIVIGGANRRQEAEKLMKGVNMLIATPGRLLDHLQNTKGFVFKNL
KALIIDEADRILEIGFEDEMRQIIKILPNEDRQSMLFSATQTTKVEDLAR
ISLRPGPLFINVQGYVVCDSDKRFLLLFSFLKRNQKKKIIVFLSSCNSVK
YYAELLNYIDLPVLELHGKQKQQKRTNTFFEFCNAERGILICTDVAARGL
DIPAVDWIIQFDPPDDPRDYIGKSLMFLTPNELGFLRYLKASKVPLNEYE
FPENKIANVQSQLEKLIKSNYYLHQTAKDGYRSYLQAYASHSLKTVYQID
KLDLAKVAKSYGFPVPPKVNITI

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): N153 R155 Q156 E159 K160 Y437 R448 N486
• Binding residue (residue number reindexed from 1): N113 R115 Q116 E119 K120 Y371 R382 N420

Enzymatic activity

• Enzyme Commision number: 3.6.4.13: RNA helicase.

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003723 RNA binding
• GO:0003724 RNA helicase activity
• GO:0004386 helicase activity
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0008186 ATP-dependent activity, acting on RNA
• GO:0016787 hydrolase activity
• GO:0016887 ATP hydrolysis activity
• GO:0042802 identical protein 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:0006364 rRNA processing
• GO:0006396 RNA processing
• GO:0030490 maturation of SSU-rRNA
• GO:0042254 ribosome biogenesis
• GO:0042273 ribosomal large subunit biogenesis
• GO:0042274 ribosomal small subunit biogenesis
• GO:1990417 snoRNA release from pre-rRNA

Cellular Component

• GO:0005634 nucleus
• GO:0005635 nuclear envelope
• GO:0005730 nucleolus
• GO:0030686 90S preribosome
• GO:0030687 preribosome, large subunit precursor
• GO:0032040 small-subunit processome

External links

• PDB: RCSB:8v84, PDBe:8v84, PDBj:8v84
• PDBsum: 8v84
• PubMed: 38632236
• UniProt: Q03532|HAS1_YEAST ATP-dependent RNA helicase HAS1 (Gene Name=HAS1)