Structure of PDB 8etj Chain C Binding Site BS01

Receptor Information

>8etj Chain C (length=325) Species: 4896 (Schizosaccharomyces pombe)

RPTVSIYNKDGSVSSETLALPFVFKAPIRPDLVRSVHTAVAKNKRQPYAV
SEKAGNMCRSGRMFAPTKTWRKWHVKVNQNEKRYAIASAVAASGVPSLLL
ARGHRIEEIPEVPLVVDDAVQSFQKTKEAVALLKEIKAYRDVIKVANSRK
LRAGKGKLRNRRHVQRRGPLVVFNEDTGIVKAFRNIPGVEIVNVRRLNLL
QLAPGGHLGRFVIWTKSAFGLLDSVFGSTTEVAQLKKNYFLPENIISNAD
VTRLINSDEIQSIVKAAGPSRVKRAHVQKKNPLKNKAVLSRLNPYAKAYK
ANVKINSEKTPKAAGEKFLSVLHEN

Ligand information

>8etj Chain 1 (length=1817)

uugaccucaaaucagguaggacuacgcgcugaacaauaagcgcaggaaaa
gaaaauaaccaugauucccucaguaacggugaagcgggaaaagcucaaau
uugaaaucuggcaacauuucuuuuguuguccgaguuguaauuucaagaag
cugcuuugaguguagacgaucggucuaaguuccuuggaacaggacgucag
agagggugagaaccccgucuuuggucgauuggauaugccauauaaagcgc
uuucgaagagucgaguuguuugcagcucuaaaugggugguaaauuucauc
uaaagcuaaauauuggcgagagaccgauagcgaacaaguagagugaucga
aagaugaaaagaacuuugaaaagagaguuaaauaguacgugaaauugcug
aaagggaagcauuggaaaucaggucagcaucaguuuucgggggcggaaaa
agaauaagggaagguggcuuuccgggaguguuuauagcccuuguuguaau
acguccacuggggacugaggacugcggcuucgugccaaggaugcugacau
aaugguuuucaauggcccgucuacacggaccaaggagucuagcaucuaug
cgaguguuugggugaugaaaacccauccgcgaaaugaaagugaaugcagg
ugggaacgcccuuguggcgugcaccaucgaccgacccggaaguauggaag
gguuugaguaagagcauagcuguugggacccgaaagauggugaaccaucu
aguagcugguuccugccgaaguuucccucaggauagcagaaacucagauc
aguuuuaugaguauguaaaaugagaguuucuagugggccauuuuugguaa
gcagaacuggcgaugcgggaugaaccgaacgugagguuaaggugccggaa
uguacgcucaucagaagaaaagguguuaguucaucuagacagcaggacgg
uggccauggaagucggaauccgcuaaggaguguguaacaacucaccugcc
gaaugaacuagcccugaaaauggauggcgcuuaagcguacuacccauacc
ucaccgucuggguugaagcucagacgaguaggcaggcguggagguuugug
acgaagccuugggcgugagccugggucgaacagccucuagugcagaucuu
gguggaaguagcauucaaaugagaacuuugaagacugaaguggggaaagg
uuccaugugaacagcaguuggacauggguuccaaggugaacagccucuag
uugauagaacaauguagauaagggaagucggcaaaaugccacugucccua
ucuacuaucuagcgaaaccacagccuggggaacgggccaggcaaaaucag
cggggcuuguggcagucaagcggcgacauugcuuuccuaucauaccgaag
cagaauucgguaagcguuggacccacuaauagggacuacugaugaagugu
cgucgcaaugguaauucaacuuaguacgagaggaaccguugauucagauc
auugguauuugcggcugccugacaaggcaaugccgcggagcuaucaucug
cuggauaacggcugaacgccucuaagccagaauccgugccagaaagcgac
gauuuuuugguccgcaugauuuauauguauaaaaauagagguaggcuacu
cuccuguaucguagaagaugggcgaugguugaugaaacggaaguguuuua
uugacuuguccaugaaauuccaaucuugugcggaaucgaauccauugcau
acgacuuuaauguggaacgggguauuguaagcagcugcugagauuaagcc
uuuguucccaagauuug

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8etj Chromatin localization of nucleophosmin organizes ribosome biogenesis.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): R33 L36 T42 K46 N47 K48 R49 Q50 Y52 V54 S55 A58 N94 M95 C96 R97 S98 R100 M101 F102 A103 P104 K106 R109 K110 K114 N116 Q117 N118 E119 R121 R140 R143 K163 T164 K165 K188 L189 R190 A191 G192 K193 K195 R197 N198 R199 R204 R205 K219 R222 N223 R234 L235 N236 P242 G243 H245 K274 K275 I293 N294 G306 P307 V310 K311 R312 H314 V315 Q316 K318 N319 N323 A325 S328 R329 A334 K335 Y337 N340 V341 K342 I343 N344 E346 T348 P349 K350 A351 A352 F356 L360 H361
• Binding residue (residue number reindexed from 1): R29 L32 T38 K42 N43 K44 R45 Q46 Y48 V50 S51 A54 N56 M57 C58 R59 S60 R62 M63 F64 A65 P66 K68 R71 K72 K76 N78 Q79 N80 E81 R83 R102 R105 K125 T126 K127 K150 L151 R152 A153 G154 K155 K157 R159 N160 R161 R166 R167 K181 R184 N185 R196 L197 N198 P204 G205 H207 K236 K237 I255 N256 G268 P269 V272 K273 R274 H276 V277 Q278 K280 N281 N285 A287 S290 R291 A296 K297 Y299 N302 V303 K304 I305 N306 E308 T310 P311 K312 A313 A314 F318 L322 H323

Gene Ontology

Molecular Function

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

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:8etj, PDBe:8etj, PDBj:8etj
• PDBsum: 8etj
• PubMed: 36423630
• UniProt: Q9P784|RL4B_SCHPO Large ribosomal subunit protein uL4B (Gene Name=rpl401)