Structure of PDB 8v87 Chain t Binding Site BS01

Receptor Information

>8v87 Chain t (length=285) Species: 1247190 (Saccharomyces cerevisiae BY4741)

LNSNPEILLRKRRNADRTRIERQELAKKKREEQIKKKRSNKNKFVRAESI
VAKTLATSREKERIKRVSILEDKKAKNETQHIASGKDFILKITEGLIREK
TTYDGKPALLFIVRVRGPLAVNIPNKAFKILSLLRLVETNTGVFVKLTKN
VYPLLKVIAPYVVIGKPSLSSIRSLIQKRGRIIYKEPHEIVLNDNNIVEE
QLGDHGIICVEDIIHEIATMGESFSVCNFFLQPFKLNREVSGFGSLNRLR
KIKQREAESRTRQFSNAATAPVIEVDIDSLLAKLN

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): L12 R24 T29 R33 A37 K40 N51 K54 G279 F280 G281 N284
• Binding residue (residue number reindexed from 1): L1 R13 T18 R22 A26 K29 N40 K43 G242 F243 G244 N247

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0042134 rRNA primary transcript binding

Biological Process

• GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0000465 exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0042254 ribosome biogenesis
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0022625 cytosolic large ribosomal subunit
• GO:0030687 preribosome, large subunit precursor

External links

• PDB: RCSB:8v87, PDBe:8v87, PDBj:8v87
• PDBsum: 8v87
• PubMed: 38632236
• UniProt: P40693|RLP7_YEAST Ribosome biogenesis protein RLP7 (Gene Name=RLP7)