Structure of PDB 8fle Chain SD Binding Site BS01

Receptor Information

>8fle Chain SD (length=225) Species: 9606 (Homo sapiens)

NFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKEYRQMYRTEIRMAR
MARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGTFV
KLNKASINMLRIVEPYIAWGYPNLKSVNELIYKRGYGKINKKRIALTDNA
LIARSLGKYGIICMEDLIHEIYTVGKRFKEANNFLWPFKLSSPRGGMKKK
TTHFVEGGDAGNREDQINRLIRRMN

Ligand information

>8fle Chain L3 (length=3372)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccggggcgcgggacauguggc
guacggaagacccgcuccccggcgccgcgggggcccaaguccuucugauc
gaggcccagcccguggacggugugaggccgguagcggcccccggcgcgcc
gggcccgggucuucccggagucggguugcuugggaaugcagcccaaagcg
ggugguaaacuccaucuaaggcuaaauaccggcacgagaccgauagucaa
caaguaccguaagggaaaguugaaaagaacuuugaagagagaguucaaga
gggcgugaaaccguuaagaggaacgggugggguccgcgcaguccgcccgg
aggauucaacccggcggcggccggccgugucggcggcccggcggaucugg
gaccgucccccgaccggcgaccggccgccgccgggcgcauuuccaccgcg
gcggugcgccgcgaccggcuccgggacggcugggaaggcccggcggggaa
gguggcucgggcccgaguguuacagcccccccggcagcagcacucgccga
aucccggggccgagggaggucgccgcgcucuccccccggggggccgggcc
accccucccacggcgcgaccgcucggggcggacuguccccagugcgcccc
gggcgggucgcgccgucgggcccggggggccacgcgcgcgucccccgaag
agggggacggcggagcgagcgcacggggucggcggcgacgucggcuaccc
acccgacccgucuugaaacacggaccaaggagucuaacacgugcgcgagu
cgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggccgcgg
ccgaggugggaucccgaggccucuccaguccgccgagggcgcaccaccgg
cccgucucgcccgccgcgccggggagguggagcacgagcgcacguguuag
gacccgaaagauggugaacuaugccugggcagggcgaagccagaggaaac
ucugguggagguccguagcgguccugacgugcaaaucggucguccgaccu
ggguauaggggcgaaagacuaaucgaaccaucuaguagcugguucccucc
gaaguuucccucaggauagcuggcgcucuccgcaguuuuauccgguaaag
cgaaugauuagagguaccuauucucaaacuuuaaauggguaagaagcccg
gcucgcuggcguggagccgggcguggaaugcgagugccuagugggccacu
uuugcagaacuggcgcugcgggaugaaccgaacgccggguuaaggcgccc
gaugccgacgcucaucagaccccaaaagguguugguugauauagacagca
ggacgguccgcuaagaccugccgaaucaacuagcccugaaaauggauggc
gcuggagcgucgggcccauacccggccgucgccggcagucgagaguggac
gggagcggcgcgcggacgcuacgccgcgacgaguaggagggccgcugcgg
ugagccuugaagccuagggcgcgggcccggguggagccgccgcaggugca
gaucuuggugguaguagcaaauauucaaacgagaacuuugaaggccgaag
uggagaaggguuccaugugaacagcaguugaacaugggucagucgguccu
gagagaugggcgagcgccguuccgaagggacgggcgauggccuccggccc
ugaucgaaagggagucggguucagauccccgaauccggaguggcggagau
gggcgccgcgaggcguccagugcgguaacgcgaccgaucccggagaagcc
ggcgggagccccggggagaguucucuuuucuuugugaagggcagggcgcc
cuggaauggguucgccccgagagaggggcccgugccuuggaaagcgucgc
gguuccggcggcguccggugagcucucgcuggcccuugaaaauccggggg
agaggguguaaaucucgcgccgggccguacccauauccgcagcaggucuc
caaggugaacagccucuggcauguuggaacaauguagguaagggaagucg
gcaagccggauccguaacuucgggauaaggauuggcucuaagggcugggu
cggucgggcuggggcgcgaagcggggucccguggaucgccccagccggcc
ggcgccuagcagccgacuuagaacuggugcggaccaggggaauccgacug
uuuaauuaaaacaaagcaucgcgaaggcccgcggcggguguugacgcgau
gugauuucugcccagugcucugaaugucaaagugaagaaauucaaugaag
cgcggguaaacggcaagugaacgagauucccacugucccuaccuacuauc
cagcgaaaccacagccaaggcgggcuuggcggaaucagcggggaaagaag
acccuguugagcuugacucuagucuggcacggugaaguuuuuucacugac
ccggugaggcggggggcuucuggcgccaagcgcccggccgcgcgccggcc
gggcgcgacccgcuccggggacagugccagguggggaguuugacuguaca
ccugucaaacgguaacgcagguguccuaaggcgagcucagggaggacaga
aaccucccguggagcagaagggcaaaagcucgcuugaucuugauuuucag
uacgaauacagaccgugaaagcggggccucacgauccuucugaccuuuug
gguuuuaagcaggaggugucagaaaaguuaccacagggaugaugucggcu
cuuccuaucauugugaagcagaauucaccaagcguuggauuguucaccca
cuaauagggaacgugagcuggguuuagaccgucgugagacagguuaguuu
uacccuacugaugauguguuguugccaugguaauccugcucaguacgaga
ggaaccgcagguucagacauuugguguaugugcuuggcugaggagccaau
ggggcgaagcuaccaucugugggauuaugacugaacgccucuaagucaga
aucccgcccaggcggaacgauagcgccgcggagccucgguuggccucgga
uagccgguccccgggguccggugcggagugcccuucguccugggaaacgg
ggcgcggccggagaggcggccgcccccucgcccgucacgcaccgcacguu
cguggggaaccuggcgcuaaaccauucguagacgaccugcuucugggucg
ggguuucguacguagcagagcagcucccucgcugcgaucuauugaaaguc
agcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8fle Principles of human pre-60S biogenesis
• Resolution: 2.48 Å
• Binding residue (original residue number in PDB): I30 R34 K35 F37 R43 R47 K48 Y51 E52 H58 K59 Y61 Y65 R66 R70 R73 M74 R76 R96 G97 N99 K104 K107 L111 R113 I117 K124 A128 N131 M132 L147 N151 R157 K161 K165 R166 E188 K202 N206 K212 L213 S214 S215 R217 G218 G219 K222 K223 R242
• Binding residue (residue number reindexed from 1): I7 R11 K12 F14 R20 R24 K25 Y28 E29 H35 K36 Y38 Y42 R43 R47 R50 M51 R53 R73 G74 N76 K81 K84 L88 R90 I94 K101 A105 N108 M109 L124 N128 R134 K138 K142 R143 E165 K179 N183 K189 L190 S191 S192 R194 G195 G196 K199 K200 R219

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003723 RNA binding
• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0042802 identical protein binding

Biological Process

• GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0014069 postsynaptic density
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8fle, PDBe:8fle, PDBj:8fle
• PDBsum: 8fle
• PubMed: 37410842
• UniProt: P18124|RL7_HUMAN Large ribosomal subunit protein uL30 (Gene Name=RPL7)