Structure of PDB 8eth Chain x Binding Site BS01

Receptor Information

>8eth Chain x (length=304) Species: 4896 (Schizosaccharomyces pombe)

KIKNKIVRQQQYMKALHQKNKDKLERRKERAKEEEKDPEKKRLRLSENIP
ATIESKRVYDETIIEDKPDEELQAELKDDEFSAYFSEERKVPKLLVTTSK
RASRKCYDFASELLDCFPNAEFRKRTGDIEVHEIAEAAAKRGYTDLLVLN
EDRKKTNALTLVHLPNGPSFYFTLSNLQTAKEISNHGRSTGHIPELIINN
FSTRLGMTVARAFQSLFIQTPQIQGRQVVTIHCQRDFLFFRRHRYAFREK
SNMPDGIGTGLQELGPRFTMRLRMVQKGVWDRKEGEVFFESNAGEESDRR
KFWL

Ligand information

>8eth Chain 1 (length=1303)

uugaccucaaaucagguaggacuacgcgcuaagcgcaggaaaagaaaaua
accaugauucccucaguaacgugaagcgggaaaagcucaaauuugaaauc
uggcaacauuucuuuuguuguccgaguuguaauuucaagaagcugcuuug
aguguagacgaucggucuaaguuccuuggaacaggacgucagagagggug
agaaccccgucuuuggucgauuggauaugccauauaaagcgcuuucgaag
agucgaguugugcagcucuaaauggguggucaucuaaagcuaaauauugg
cgagagaccgauagcgaacaaguagagugaucgaaagaugaaaagaacuu
ugaaaagagaguuaaauaguacgugaaauugcugaaagcauuggaaauca
gucuuaccugggugagaucaguagucucucgagacuaugcacucugaacc
ugugguaggucagcaucaguuuucgggggcggaaaaagaauaagggaagg
uggcuguuuauagcccuuguuguaauacguccacuggggacugaggacug
cggcuucgugccaaggaugcugacauaaugguuuucaauggcccguccac
ggaccaaggagucuagcaucuaugcgaguguuugggugaugaaaacccau
ccgcgaggugggaacgcccuggcgugcaccaucagagcauagcuguuggg
acccgaaagauggugaaccaucuaguagcugguuccugccgaagagcaga
aacucagaucaguuuuaaaugagaguuucuagugggccauuacuggcgau
gcgggccgaacgugagguuaaggugccggaauguacgcuagaaagguguu
aguuaacuagcccugggcgcuuaagcguacuacccauaccucaccgucug
gguuagcuuugagaagcucagacgaguaggcaggcguggagguuugugac
gaagccuugggcgugagccugggucgaacagccucuagugcagaucuugg
uggaaguagcagcgaaaccacagccugggggccaggucgucgcaauggua
auucaacuuaguacggaaccguugauucagaucauugguagagcuaucau
cugccggauaacggcugagccagaauccgugccagagcgacgauauguau
aaaaauagaggucucuccuguaucguagaagaugggcgaugguugaugaa
acggaaguguuuuauugacuuguccaugaaauuccagaauccauugcaua
cgacuuuaauguggaacgggguauuguagauuaagccuuuguucccaaga
uuu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8eth Chromatin localization of nucleophosmin organizes ribosome biogenesis.
• Resolution: 3.8 Å
• Binding residue (original residue number in PDB): K5 N6 K7 I8 V9 R10 Y14 L26 R29 R46 N50 P52 A53 T54 I55 R103 R106 D130 K156 S299 R301 R302
• Binding residue (residue number reindexed from 1): K3 N4 K5 I6 V7 R8 Y12 L24 R27 R44 N48 P50 A51 T52 I53 R101 R104 D128 K154 S297 R299 R300

Gene Ontology

Molecular Function

• GO:0019843 rRNA binding
• GO:0042134 rRNA primary transcript 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:0180023 cytosolic large ribosomal subunit assembly
• GO:1902626 assembly of large subunit precursor of preribosome

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005732 sno(s)RNA-containing ribonucleoprotein complex
• GO:0030687 preribosome, large subunit precursor

External links

• PDB: RCSB:8eth, PDBe:8eth, PDBj:8eth
• PDBsum: 8eth
• PubMed: 36423630
• UniProt: O14180|YDS4_SCHPO Brix domain-containing protein C4F8.04 (Gene Name=SPAC4F8.04)