Structure of PDB 8etc Chain j Binding Site BS01

Receptor Information

>8etc Chain j (length=75) Species: 4896 (Schizosaccharomyces pombe)

MRHNKSHTICRRCGKRSFHIQKSTCACCGYPAAKTRSYNWGAKAKRRRTT
GTGRMSYLKKVHRSFKNGFRSGKPA

Ligand information

>8etc Chain 1 (length=2140)

auuugaccucaaaucagguaggacuacgcgcugaacucaauaagcgcagg
aaaagaaaauaaccaugauucccucaguaacggugaagcgggaaaagcuc
aaauuugaaaucuggcaacauuucuuuuguuguccgaguuguaauuucaa
gaagcugcuuugaguguagacgaucggucuaaguuccuuggaacaggacg
ucagagagggugagaaccccgucuuuggucgauuggauaugccauauaaa
gcgcuuucgaagagucgaguuguuugcagcucuaaauggguggucaucua
aagcuaaauauuggcgagagaccgauagcgaacaaguagagugaucgaaa
gaugaaaagaacuuugaaaagagaguuaaauaguacgugaaauugcugaa
agggaagcauuggaaaucaggucagcaucaguuuucgggggcggaaaaag
aauaagggaagguggcuguuuauagcccuuguuguaauacguccacuggg
gacugaggacugcggcuucgugccaaggaugcugacauaaugguuuucaa
uggcccgucuacacggaccaaggagucuagcaucuaugcgaguguuuggg
ugaugaaaacccauccgcgaaaugaaagugaaugcaggugggaacgcccu
ggcgugcaccaucgaccgacccggaaggguuugaguaagagcauagcugu
ugggacccgaaagauggugaacuaugccugaauagggugaagccagagga
aacucugguggaggcucguuuggguauaggggcgaaagacuaaucgaacc
aucuaguagcugguuccugccgaaggcagaaacucagaucaguuuuaugu
guaaaaugagaguuucuagugggccauuuuugguaagcagaacuggcgau
gcgggaugaaccgaacgugagguuaaggugccggaauguacgcucaucag
acaccagaaaagguguuaguucaucuagacagcaggacgguggccaugga
agucggaauccgcuaaggaguguguaacaacucaccugccgaaugaacua
gcccugaaaauggauggcgcuuaagcguacuacccauaccucaccgucug
gguuagaagcucagacgaguaggcaggcguggagguuugugacgaagccu
ugggcgugagccugggucgaacagccucuagugcagaucuugguggaagu
agcaaauauucaaaugagaacuuugaagacugaaguggggaaagguucca
ugugaacagcaguuggacauggguuagucgauccuaagagauagggaagc
uccguaugaaaaucgaaagggaauccgguuaauauuccggaaccagaagg
uggaacacggcaacguaaaugaaguuggagacgucggcgggagcccuggg
aagaguucucuuuucuuuuuaacaaaccacacccugaaaucgguuuaucc
ggagcuaggguaugguguuuggaagaguucagcgccucaugcugaauccg
gugcgcucucgacggccuugaaaauccaacggaaguuucacaucuggucg
uacucauaaccgcagcaggucuccaaggugagccucuaguugauagaaca
auguagauaagggaagucggcaaaaugggaaucgauucccacugucccua
ucuacuaucuagcgaaaccacagccuggggaacgggccaggcaaaaucag
cgggguggcuuguggcagccaagcgcgacguugcuggcucuuccuaucau
accgaagcagaauucgguaagcguuggacccacuaauagggagcuggguu
ccuacugaugaagugucgucgcaaugguaauucaacuuaguacgagagga
accguugauucagaucauugguauuugcggcugccugacaaggcaaugcc
gcggagcuaucaucugccggauaacggcugaacgccucuaagccagaauc
cgugccagaaagcgacgauuguauaaaaauagaggucucuccuguaucgu
agaagaugggcgaugguugaugaaacggaaguguuuuauugacuugucca
ugaaauuccagaauccauugcauacgacuuuaauguggaacgggguauug
uaagcagcugcugagauuaagccuuuguucccaagauuug

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8etc Chromatin localization of nucleophosmin organizes ribosome biogenesis.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): R11 H12 N13 K14 S15 H16 R25 S26 H28 Q30 A35 K43 T44 R45 Y47 N48 W49 K52 A53 R55 R56 H71 G77 S80 G81
• Binding residue (residue number reindexed from 1): R2 H3 N4 K5 S6 H7 R16 S17 H19 Q21 A26 K34 T35 R36 Y38 N39 W40 K43 A44 R46 R47 H62 G68 S71 G72

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0008270 zinc ion binding
• GO:0019843 rRNA binding
• GO:0046872 metal ion binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

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:8etc, PDBe:8etc, PDBj:8etc
• PDBsum: 8etc
• PubMed: 36423630
• UniProt: P05733|RL37B_SCHPO Large ribosomal subunit protein eL37B (Gene Name=rpl3702)