Structure of PDB 8eug Chain N Binding Site BS01

Receptor Information

>8eug Chain N (length=200) Species: 4896 (Schizosaccharomyces pombe)

GAYKYLEELAKKKQSDVNLFLSRVRAWEYRQMNVIHRASRPSRPDKARRL
GYKAKQGYVIYRIRVRRGGRKRPVPKGQTYGKPVHQGVNHLKYQRSARCT
AEERVGRYCSNLRVLNSYWVNQDATYKFFEVILVDPSHKAIRRDPRINWI
VNPVHKHRESRGLTSIGKKSRGIGKGHRFNNSPQHATWLRHNTLSLRRYR

Ligand information

>8eug Chain 1 (length=2869)

uugaccucaaaucagguaggacuacgcgcugaacuuaagcauaucaauaa
gcgcaggaaaagaaaauaaccaugauucccucaguaacggcgagugaagc
gggaaaagcucaaauuugaaaucuggcaacauuucuuuuguuguccgagu
uguaauuucaagaagcugcuuugaguguagacgaucggucuaaguuccuu
ggaacaggacgucagagagggugagaaccccgucuuuggucgauuggaua
ugccauauaaagcgcuuucgaagagucgaguuguuugggaaugcagcucu
aaaugggugguaaauuucaucuaaagcuaaauauuggcgagagaccgaua
gcgaacaaguagagugaucgaaagaugaaaagaacuuugaaaagagaguu
aaauaguacgugaaauugcugaaagggaagcauuggaaaucagucuuacg
uaggucagcaucaguuuucgggggcggaaaaagaauaagggaagguggcu
guuuauagcccuuguuguaauacguccacuggggacugaggacugcggcu
ugccaaggaugcugacauaaugguuuucaauggcccgucuugaaacacgg
accaaggagucuagcaucuaugcgaguguuugggugaaaaacccauccgc
gaaaugaaagugaaugcaggugggaacgcccuggcgugcaccaucgaccg
acccggaaguuugucaauggaaggguuugaguaagagcauagcuguuggg
acccgaaagauggugaacuaugccugaauagggugaagccagaggaaacu
cugguggaggcucguagagauucugacgugcaaaucgaucuucaaauuug
gguauaggggcgaaagacuaaucgaaccaucuaguagcugguuccugccg
aaguuucccucaggauagcagaaacucagaucaguuuuaugagguaaagc
gaaugauuagagguaccuauucucaaacuuuaaauauguaagacgcccuu
gucgcuuaauuggacgugggccaucgaaugagaguuucuagugggccauu
uuugguaagcagaacuggcgaugcgggaugaaccgaacgugagguuaagg
ugccggaauguacgcucaucagacaccagaaaagguguuaguucgaacua
gcccugaaaauggauggcgcuuaagcguacuacccauaccucaccgucug
gguuaagaagcucagacgaguaggcaggcguggagguuugugacgaagcc
uugggcgugagccugggucgaacagccucuagugcagaucuugguggaag
uagcaaauauucaaaugagaacuuugaagacugaaguggggaaagguucc
augugaacagcaguuggacauggguuagucgauccuaagagauagggaag
cuccguaugaaaggcacgauuuuucgugccuaucgaaagggaauccgguu
aauauuccggaaccagaagguggaaucaacacggcaacguaaaugaaguu
ggagacgucggcgggagcccugggaagaguucucuuuucuuuuuaacaaa
ccacacccugaaaucgguuuauccggagcuaggguaugguguuuggaaga
guucagcggcugaauccggugcgcucucgacggcccuugaaaauccaacg
gaaguuguuuucacaucuggucguacucauaaccgcagcaggucuccaag
gugaacagccucuaguugauagaacaauguagauaagggaagucggcaaa
auggauccguaacuucgggauaaggauuggcucuaaggguaucaacuuag
aacugguacggacaaggggaaucugacugucuaauuaaaacauagcauug
cgauggccagaaagugguguugacgcaaugugauuucugcccagugcucg
aaugucaaagugaagaaauucaaccaagcgcggguaaacggcaagguagc
caaaugccucgucaucuaacuagugacgcgcaugaauggauuaacgagau
ucccacugucccuaucuacuaucuagcgaaaccacagccuggggaacggg
ccaggcaaaaucagcggggaaagaagacccuguugagcuugacucuaguu
ugacauugugaauuuacuuaaucaaugaagcggaauuucuagcguuaaag
uuucgcgaacugauccgcguugaugacauugucagguggggaguuuggcu
ggggcggcacaucuguuaaaagauaacgcagguguccuaagggggacuca
ucgagaaucucgaguagaauaaaaggguaaaaguccccuugauuuugauu
uucagugugaauacaaaccaugaaaguguggccuaucgauccuuuguucc
cucgaaauuugaggacagaggugccagaaaaguuaccacagggauaacug
gcuucagccaagacguugcauucuucgaugucggcucuuccuaucauacc
gaauucgguaagcguuggauuguucacccacuaauagggaacgugagcug
gguuuagaccgucgugagacagguuaguuuuacccuacugaugaaguguc
gucgcaaugguaauucaacuuaguacgggaaccguugauucagaucauug
guauuugcggcugccugacaaggcaaugccgcggagcuaucaucugccgg
auaacggcugagccagaauccgugccagaaagcgacgauuuauguauaaa
aauagagguaacucuccuguaucguagaagaugggcgaugguugaacgga
aguguuuugacuuguccaugaaauuccagaauccauugcauacgacuuua
auguggaacgggguauuguaagcaguagagucgaucugcugagauuaagc
cuuuguucccaagauuugu

........................<<<<<<.....<......>......>
>>>>.>.........<<....>>..<<<<<......<<.....>>.....
>>>>>..<<<...........<<.<<<<<<<.......>>>>>>>.>>..
...........<<<<<.<<<<<..<<<<<..<<<<<<<<<.....<<<<.
.....>>>>.((......<<<.....))>>>......>>>>>>>>>..>>
>>>.....>>>>>>>>.>>........<<<<<<<........>>>>>>>.
....<<<<<..((((((>>>>>..>>>.......................
...........<<....>>...............<<<<....>>>>....
..............................<<<<<<<<<<<.<...<<..
>>.<<<<<<<.<<<<<<<<<<<<<<<.....<.<<<<<<<<......<..
.>......>>>>>>>>....>.>>>>>.>>>>>>>>>>........<<<.
.>>>.....>>>>>>>....>>>>>>>>>>>>..<<<<........>>>>
<<<<<<....<<<<<<.<<<<<<..<<<...<<<<.....>>>>...>>>
...<<....>>.......<<<<<..<<<<<..>>>>>...>>>>>.<<<<
<<<<....<<<....>>>....>>>.>>>.>>....>>>>>>.>>>>>>.
.<<.<...<<<<<<.....<<<<<<<<<..<<<....<<<<<<<....>>
>>>>>.....>>>...<<<..<<.<<........>>>>.>>>....>>>>
>>>>>...<<.......>>......>>>>>>......>.>>..<<<<<<.
...<.<<<....>>>.><<<<<<<<<<...<<<.<<<<<<<.....<<<.
...<<<....<<<..>>>....>>>..>.>>.....>>>>>...<<<<.<
<<<.<......>>>>>.>>>>.....>>>>>>>>>>>>>.>>..<<<<.<
<<<<.....>>>>>.>>>>....<<<......>>>...<<<<<<<...<<
<(((.....<<<<<<.....<<..........<<<.<<<<<<<..>>>>>
>>>>>..........))).>>...>>>>>>.>>>...>>>>>>><<<<<<
<<<......>>>>>>>>>....>>>>>>..<<<<<<<<.<<......<<<
<.<<<<....>>>>>>>>...>>>>>>>>>>........>>>>>><<...
..<<.....<<<<<<.......>>>>>><<<<.....<<<<<.<<...<<
<<<<...<<.....>>.>>>>>>....((<<<<<<...<<....<<<...
.>>>........<<<<<<......>>>>>>..>>....>>...<<<<<..
......>>>>>))<<<<..<<<<<<<....<<<....>>>.....((<<<
<<<...<<<<.<<<<<<<.<<<<<<<<<<...[[..>>>>>>....<<<<
<...<<<<<<....<<<.....>>>....>>>>>>.....>>>>>.....
<<<<<<<.>>>>>>>>>>>...>>>>>>>.>>>>.........>>>>>>.
......>>>>.>>>.>>>>>>>>..>>.....<<......>>>>>>>.<<
<<.....>>>>..>>>>..<<<<.....<<<<<<<.<<............
...<<<<<...............>>>>><<.<<<<<<<<..>>..>>>>>
>.>>............<<<<<<<<<..<<<.........>>>..<<<<<<
<....<<<<.....>>>>......>>>>>>>...<<...<<..<<<<<<<
..<<<....<<<<<....>>>>.>...>>>>>>>>..>>>>.......<.
..........<<<<<.......>>>>>.....>.....>>....>>.>>>
>>>>.....>>.>>>>>>>..>>>>>>....>>....<<<<<........
>>>>>....<<<<<..<<<.<<......<<<<.<<<<<<..<<<<<.<<<
<<<<<..<<<<..>>>>...<<<<<.....<<<<..........))..<<
<<<...>>>>>..>>>>..>>>>>.....>>>>>>>>..>>>>>...<<<
.....>>>..<<<<<<...........>>>>>>..<<...<<<<<<<...
<<<<<<.>>>>>>.....<<...(((>>....>>>>>>>...<<<..<<<
<.......>>>>..>>>.<<<....>>>.>>)))......<<<<<<<..<
<<<.))))))>>>>>>>>>>>.........>>>>..>>>>>>.......<
<...<<<<......>>>>..>.>.......<<<<<.<<<<<<..<.<<<<
<<..>>>>>>...>.<<<.........>>>.....>>>>>..>...>>>.
>>....<<<<<<<....>>>.>>>>....>>..>>>.>>>>>.....<<<
<<<<<..<<<<...<<<<<..............>>>>>..<<<<<...<<
<<....<<<<<<<<<<]]..>>>>>..>>>>>...>>>>..>>>>>.<<<
<....<<<<.>>>>....>>>>.>>>>....>>>>>>>>......<<...
....<<<<....>>>>....>>........<<<<<....<<<<.<<<...
...>>>..>>>>..>>>>>.........<<<<<.<.............>.
....<<<<<<<<<.<<<....<<<<....<.>...>>>>...>>>....>
>>>.>>>>>...>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8eug Chromatin localization of nucleophosmin organizes ribosome biogenesis.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): G2 Y4 K5 E8 K12 K14 Q15 R24 W28 R31 N34 V35 S40 R41 R44 K47 R49 R50 L51 K54 A55 Q57 R67 R68 G69 G70 R71 K72 R73 P74 P76 K77 Q79 Y81 G82 K83 V85 H86 Q87 V89 N90 H91 K93 Y94 Q95 S97 R105 R108 S111 N112 W120 A125 Y127 S138 K140 R144 R147 W150 P154 V155 H156 K157 H158 S161 R162 L164 S166 K169 K170 S171 R172 I174 K176 G177 H178 R179 N181 Q185 W189 R191 H192 S196 R198 R199 Y200 R201
• Binding residue (residue number reindexed from 1): G1 Y3 K4 E7 K11 K13 Q14 R23 W27 R30 N33 V34 S39 R40 R43 K46 R48 R49 L50 K53 A54 Q56 R66 R67 G68 G69 R70 K71 R72 P73 P75 K76 Q78 Y80 G81 K82 V84 H85 Q86 V88 N89 H90 K92 Y93 Q94 S96 R104 R107 S110 N111 W119 A124 Y126 S137 K139 R143 R146 W149 P153 V154 H155 K156 H157 S160 R161 L163 S165 K168 K169 S170 R171 I173 K175 G176 H177 R178 N180 Q184 W188 R190 H191 S195 R197 R198 Y199 R200

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