Structure of PDB 8v83 Chain v Binding Site BS01

Receptor Information

>8v83 Chain v (length=149) Species: 1247190 (Saccharomyces cerevisiae BY4741)

SVRKRKMNRSSVGKATRRNKDKQRKINIQSNPIIAANWDYSLTMAQNYKK
LGLRAKLQTPAGGKEADLSKVVKRIPLTEVVKKLEELASRPVIRKERSQS
EREEEWLEKLYKKHGDDYKKMFFDKKLNIYQQSEGDLKRRLLRWKKRNG

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): S3 R5 K6 R7 K16 A17 T18 R19 K22 R26 N29 Q31 S32 T45 Q48 A63 G64 G65 E67 R172 R175 S176 S178 R180 E181 W184 Y208 Q210 S211 E212 G213 K216 R217 R218
• Binding residue (residue number reindexed from 1): S1 R3 K4 R5 K14 A15 T16 R17 K20 R24 N27 Q29 S30 T43 Q46 A61 G62 G63 E65 R94 R97 S98 S100 R102 E103 W106 Y130 Q132 S133 E134 G135 K138 R139 R140

Gene Ontology

Molecular Function

• GO:0003674 molecular_function
• GO:0005515 protein binding

Biological Process

• GO:0006364 rRNA processing
• GO:0042254 ribosome biogenesis
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0030687 preribosome, large subunit precursor
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8v83, PDBe:8v83, PDBj:8v83
• PDBsum: 8v83
• PubMed: 38632236
• UniProt: P40007|NOP16_YEAST Nucleolar protein 16 (Gene Name=NOP16)