Structure of PDB 8v87 Chain r Binding Site BS01

Receptor Information

>8v87 Chain r (length=214) Species: 1247190 (Saccharomyces cerevisiae BY4741)

PQNDYIERHIKQHGKRLDHEERKRKREARESHKISERAQKLTGWKGKQFA
KKRYAEKVSMRKKIKAHEQSKVKNTAKAISSSIKQKRLEKADKFSVPLPK
VRGISEEEMFKRMITKHTFVGEGFTRRPVKMERIIRPSALRQKKANVTHP
ELGVTVFLPILAVKKNPQSPMYTQLGVLTKGTIIEVNVSELVWGKYAQVT
NEPDRDGCVNAVLL

Ligand information

>8v87 Chain 1 (length=2489)

guuugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaau
aagcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaa
gcggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguugua
auuuggagagggcaacuuuggggccguuccuugucuauguuccuuggaac
aggacgucauagagggugagaaucccguguggcgaggagugcgguucuuu
guaaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugg
gugguuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaagu
acagugauggaaagaugaaaagaacuuugaaaagagagugaaaaaguacg
ugaaauuguugaaagggaagggcauuugaucagacauggugcacugggcc
agcaucaguuuugguggcaggauaaauccauaggaauguagcuugccucg
guaaguauuauagccugugggaauacugccagcugggacugaggacugcg
acguaagucaaggaugcuggcauaaugguuauaugccgcccgucuugaaa
cacggaccaaggagucuaacgucuaugcgaguguuuggguguaaaaccca
uacgcguaaugaaagugaacguagguuggggccucgcaagaggugcacaa
ucgaccgaguaagagcauagcuguugggacccgaaagauggugaacuaug
ccugaauagggugaagccagaggaaacucugguggaggcucgcgguucga
ucgucgaauuuggguauaggggcgaaagacuaaaaccaucuaguagcugg
uuccugccgaaguuucccucaggauagcagaagcucguaucaguuuuaug
aauguaaaaugaagagcuuuuagugggccauuuuugguaagcagaacugg
cgaugcgggaugaaccgaacguagaguuaaggugccggaauacacgcuca
ucagacacaaaagguguuaguucaucuagacagccggacgguggccaugg
aagucggaauccgcuaaggaguguguaacaacucaccggccgaaugaacu
agcccugaaaauggauggcgcucaagcguguuaccuauacucuaccguca
ggguugaugcccugacgaguaggcaggcguggaggucagugacgaagccu
agaccguaaggucgggucgaacggccucuagugcagaucuuggugguagu
agcaauucaaaugagaacuuugaagacugaaguggggaaagguuccacgu
caacagcaguuggacguggguuagucgauccuaagagauggggaagcucc
guuucaaaggccugauuuuaugcaggccaccaucgaaagggaauccgguu
aagauuccggaaccuggauauggauucuucacgguaacguaacugaaugu
ggagacgucggcgcgagcccugggaggaguuaucuuuucuucuuaacagc
uuaucaccccggaauugguuuauccggagauggggucuuauggcuggaag
aggccagcaccuuugcuggcuccggugcgcuugugacggcccgugaaaau
ccacaggaaggaauaguuuucaugccaggucguacugaucuccaagguga
acagccucuaguugauagaauaauguagauaagggaagucggggggaauc
uggagauucccacugucccuaucuacuaucuagcgaaaccacagccaagg
gaacgggcuuggcagaaucagcggggaaagaagacccuguugagcuugac
ucuaguuugacauugugaagagacauagaggguguagaauaagugggagc
uucggcgccagugaaauaccacuaccuuuauaguuucuuuacuauuguca
gguggggaguaaaguuaccacagggauaacuggcuuguggcagucaagcg
agcgacauugcuuuuugagaugucggcucuuccuaucauaccgaagcaga
auucgguaagcguuggauuguucacccacuaauagggaacgugagcuggg
uuuagaccgucgugagacagguuaguuuuacccuacugaugaauguuacc
gcaauaguaauugaacuuaguacgagaggaacaguucauucggauaauug
guuuuugcggcugucugaucaggcauugccgcgaagcuaccauccgcugg
auuauggcugaacgccucuaagucagaauccaugcuagaacgcggugauu
ucuuugcuccacacaauauagauggauacgaauaaggcguccuuguggcg
ucgcugaaccauagcaggcuagcaacggugcacuuggcggaaaggccuug
ggugcuugcuggcgaauugcaaugucauuuugcguggggauaaaucauuu
guauacgacuuagauguacaacgggguauuguaagcaguagaguagccgu
uacgaucugcugagauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8v87 The DEAD-box ATPase Dbp10/DDX54 initiates peptidyl transferase center formation during 60S ribosome biogenesis.
• Resolution: 2.66 Å
• Binding residue (original residue number in PDB): P2 D5 Y6 I7 E8 R23 R25 K26 A29 R30 H33 S36 A39 Q40 L42 T43 G44 W45 K46 K48 A51 K52 R54 Y55 K58 S104 K108 K167 N183 T192 P207 T246 N247 R251 D252 N256
• Binding residue (residue number reindexed from 1): P1 D4 Y5 I6 E7 R22 R24 K25 A28 R29 H32 S35 A38 Q39 L41 T42 G43 W44 K45 K47 A50 K51 R53 Y54 K57 S80 K84 K130 N146 T155 P170 T200 N201 R205 D206 N210

Gene Ontology

Molecular Function

• GO:0003674 molecular_function
• GO:0005515 protein binding

Biological Process

• GO:0000460 maturation of 5.8S rRNA
• 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:0000470 maturation of LSU-rRNA
• 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

External links

• PDB: RCSB:8v87, PDBe:8v87, PDBj:8v87
• PDBsum: 8v87
• PubMed: 38632236
• UniProt: P40078|NSA2_YEAST Ribosome biogenesis protein NSA2 (Gene Name=NSA2)