Structure of PDB 8esr Chain N Binding Site BS01

Receptor Information

>8esr Chain N (length=165) Species: 4896 (Schizosaccharomyces pombe)

GAYKYLEELAKKKQSDVNLFLSRVRAWEYRQMNVIHRASRPSRPDKARRL
GYKAKQGYVIYRIRVRRGRSARCTAEERVGRYCSNLRVLNSYWVNQDATY
KFFEVILVDPSHKAIRRDPRINWIVNPVHKHRESRGLTSIGKKSRGIGKG
HRFLRHNTLSLRRYR

Ligand information

>8esr Chain 1 (length=2143)

uugaccucaaaucagguaggacuacgcgcugaacaauaagcgcaggaaaa
gaaaauaaccaugauucccucaguaacggugaagcgggaaaagcucaaau
uugaaaucuggcaacauuucuuuuguuguccgaguuguaauuucaagaag
cugcuuugaguguagacgaucggucuaaguuccuuggaacaggacgucag
agagggugagaaccccgucuuuggucgauuggauaugccauauaaagcgc
uuucgaagagucgaguugugcagcucuaaaugggugguucaucuaaagcu
aaauauuggcgagagaccgauagcgaacaaguagagugaucgaaagauga
aaagaacuuugaaaagagaguuaaauaguacgugaaauugcugaaaggga
agcauuggaaaucaggucagcaucaguuuucgggggcggaaaaagaauaa
gggaagguggcuguuuauagcccuuguuguaauacguccacuggggacug
aggacugcggcuugccaaggaugcugacauaaugguuuucaauggcccgu
cuugaaacacggaccaaggagucuagcaucuaugcgaguguuugggugau
gaaaacccauccgcgaaauggugaaugcaggugggaacgcccuggcgugc
accaucgaccguaagagcauagcuguugggacccgaaagauggugaacua
ugccugaauuggguauaggaaccaucuaguagcugguuccugccgaaguu
uccggauagcagaaacucagaucaguuuuauguguaaaaugagaguuucu
agugggccauuuuugguaagcagaacuggcgaugcgggaugaaccgaacg
ugagguuaaggugccggaauguacgcucaucagagaaaagguguuaguuc
aucuagacagcaggacgguggccauggaagucggaauccgcuaaggagug
uguaacaacucaccugccgaaugaacuagcccugaaaauggauggcgcuu
aagcguacuacccauaccucaccgucuggguuagagaagcucagacgagu
aggcaggcguggagguuugugacgaagccuugggcgugagccugggucga
acagccucuagugcagaucuugguggaaguagcauucaaaugagaacuuu
gaagacugaaguggggaaagguuccaugugaacagcaguuggacaugggu
uagucgauccuaagagauagggaagcuccguaugaaaguugcacgauuuu
ucgugccuaucgaaagggaauccgguuaauauuccggaaccagaaggugg
aaucacggcaacguaaaugaaguuggagacgucggcgggagcccugggaa
gaguucucuuuucuuuuuaacaaaccacacccugaaaucgguuuauccgg
agcuaggguaugguguuuggaagaguucagcggcugaauccggugcgcuc
ucgacggcccuugaaaauccaacggaagguuuucacaucuggucguacuc
cuccaaggugccucuaguugauagaacaauguagauaagggaagucggca
aaaugggcccacugucccuaucuacuaucuagcgaaaccacagccugggg
aacgggccaggcaaaaucagcggcccuguugagcuugacucuaguuugca
gguggggaguuaaaguuaccacagggaucuuguggcagccaagcgcgacg
uugcuucggcucuuccuaucauaccgaagcagaauucgguaagcguugga
cccacuaauagggaacgugagcugggaccgucgugagacgguuagucuac
ugaugaagugucgucgcaaugguaauucaacuuaguacgagaggaaccgu
ugauucagaucauugguauuugcggcugccugacaaggcaaugccgcgga
gcuaucaucugccggauaacggcugaacgccucuaagccagaauccgugc
cagaaagcgacgauauguauaaaaauagagguaggcuacucuccuguauc
guagaagaugggcgaugguugaugaaacggaaguguuuuauugacuuguc
caugaaauuccaugaauccauugcauacgacuuuaauguggaacggggua
uuguaagcagcugcugagauuaagccuuuguucccaagauuug

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8esr Chromatin localization of nucleophosmin organizes ribosome biogenesis.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): G2 Y4 K5 K12 K14 Q15 N34 V35 S40 R41 R44 K47 R49 R50 L51 K54 A55 K56 Q57 R67 R68 G69 R96 S97 R105 R108 N112 N117 W120 Y127 S138 H139 K140 A141 R144 R147 W150 P154 V155 H156 K157 H158 R159 S161 R162 L164 S166 K169 K170 R172 I174 K176 G177 H178 R179 R191 H192 R198 R199 Y200 R201
• Binding residue (residue number reindexed from 1): G1 Y3 K4 K11 K13 Q14 N33 V34 S39 R40 R43 K46 R48 R49 L50 K53 A54 K55 Q56 R66 R67 G68 R69 S70 R78 R81 N85 N90 W93 Y100 S111 H112 K113 A114 R117 R120 W123 P127 V128 H129 K130 H131 R132 S134 R135 L137 S139 K142 K143 R145 I147 K149 G150 H151 R152 R155 H156 R162 R163 Y164 R165

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:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8esr, PDBe:8esr, PDBj:8esr
• PDBsum: 8esr
• PubMed: 36423630
• UniProt: O74895|RL15A_SCHPO Large ribosomal subunit protein eL15A (Gene Name=rpl15)