Structure of PDB 8v87 Chain F Binding Site BS01

Receptor Information

>8v87 Chain F (length=215) Species: 1247190 (Saccharomyces cerevisiae BY4741)

RAARKAANKEKRAIILERNAAYQKEYETAERNIIQAKRDAKAAGSYYVEA
QHKLVFVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVTKATLELLKL
IEPYVAYGYPSYSTIRQLVYKRGFGKINKQRVPLSDNAIIEANLGKYGIL
SIDDLIHEIITVGPHFKQANNFLWPFKLSNPSGGWGVPRKFKHFIQGGSF
GNREEFINKLVKSMN

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): R30 R33 N37 R41 R60 I63 R67 K70 G91 I92 N93 K94 P97 K98 K101 L105 R107 R110 I111 N112 K121 A122 E125 L126 S142 R145 R151 K155 K158 Q159 R160 K196 N200 K206 L207 S208 N209 P210 S211 W214 R218 K219 K241
• Binding residue (residue number reindexed from 1): R1 R4 N8 R12 R31 I34 R38 K41 G62 I63 N64 K65 P68 K69 K72 L76 R78 R81 I82 N83 K92 A93 E96 L97 S113 R116 R122 K126 K129 Q130 R131 K167 N171 K177 L178 S179 N180 P181 S182 W185 R189 K190 K212

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0000470 maturation of LSU-rRNA
• GO:0002181 cytoplasmic translation
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8v87, PDBe:8v87, PDBj:8v87
• PDBsum: 8v87
• PubMed: 38632236
• UniProt: P05737|RL7A_YEAST Large ribosomal subunit protein uL30A (Gene Name=RPL7A)