Structure of PDB 8fl3 Chain SD Binding Site BS01

Receptor Information

>8fl3 Chain SD (length=225) Species: 9606 (Homo sapiens)

NFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKEYRQMYRTEIRMAR
MARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGTFV
KLNKASINMLRIVEPYIAWGYPNLKSVNELIYKRGYGKINKKRIALTDNA
LIARSLGKYGIICMEDLIHEIYTVGKRFKEANNFLWPFKLSSPRGGMKKK
TTHFVEGGDAGNREDQINRLIRRMN

Ligand information

>8fl3 Chain L3 (length=3494)

gcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguca
gcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaaca
gggaagagcccagcgccgaauccccgccccggggcgcgggacauguggcg
uacggaagacccgcuccccggcgccgcgggggcccaaguccuucugaucg
aggcccagcccguggacggugugaggccgguagcggcccccggcgcgccg
ggcccgggucuucccggagucggguugcuugggaaugcagcccaaagcgg
gugguaaacuccaucuaaggcuaaauaccggcacgagaccgauagucaac
aaguaccguaagggaaaguugaaaagaacuuugaagagagaguucaagag
ggcgugaaaccguuaagagguaaacgggugggguccgcgcaguccgcccg
gaggauucaacccggcggcggccggccgugucggcggcccggcggaucug
ggaccgucccccgaccggcgaccggccgccgccgggcgcauuuccaccgc
ggcggugcgccgcgaccggcuccgggacggcugggaaggcccggcgggga
agguggcucgggcccgaguguuacagcccccccggcagcagcacucgccg
aaucccggggccgagggagucgccgcgcucuccccccggggggccgggcc
accccucccacggcgcgcgccgucgggcccggggggccacgcgcgcgucc
cccgaagagggggacggcggagcgagcgcacggggucggcggcgacgucg
gcuacccacccgacccgucuugaaacacggaccaaggagucuaacacgug
cgcgagucgggggcucgcacgaaagccgccguggcgcaaugaaggugaag
gccgcggccgaggugggaucccgaggcccgccgagggcgcaccaccggcc
cgucucgcccgccgcgccggggagguggagcacgagcgcacguguuagga
cccgaaagauggugaacuaugccugggcagggcgaagccagaggaaacuc
ugguggagguccguagcgguccugacgugcaaaucggucguccgaccugg
guauaggggcgaaagacuaaucgaaccaucuaguagcugguucccuccga
aguuucccucaggauagcuggcgcucuccgcaguuuuauccgguaaagcg
aaugauuagaggucuuggggccggaucucaaccuauucucggguaagaag
cccggcucgcuggcguggagccgggcguggaaugcgagugccuagugggc
cacuuuugguaagcagaacuggcgcugcgggaugaaccgaacgccggguu
aaggcgcccgaugccgacgcucaucagaccccagaaaagguguugguuga
uauagacagcaggacgguggccauggaagucggaauccgcuaaggagugu
guaacaacucaccugccgaaucaacuagcccugaaaauggauggcgcugg
agcgucgggcccauacccggccgucgccggcagugacgcuacgccgcgac
gaguaggagggccgcugcggugagccuugaagccuagggcgcgggcccgg
guggagccgccgcaggugcagaucuuggugguaguagcaaauauucaaac
gagaacuuugaaggccgaaguggagaaggguuccaugugaacagcaguug
aacaugggucagucgguccugagagaugggcgagcgccguuccgaaggga
cgggcgauggccuccggcccucgaucgaaagggagucggguucagauccc
cgaauccggaguggcggagaugggcgccgcgaggcguccagugcgguaac
gcgaccgaucccggagaagccggcgggagccccggggagaguucucuuuu
cuuugugaagggcagggcgcccuggaauggguucgccccgagagaggggc
ccgugccuuggaaagcgucgcgguuccggcggcguccggugagcucucgc
uggcccuugaaaauccgggggagaggguguaaaucucgcgccgggccgua
cccauauccgcagcaggucuccaaggugaacagccucuggcauguuggaa
caauguagguaagggaagucggcaagccggauccguaacuucgggauaag
gauuggcucuaagggcugggucggucgggcuggggcgcgaagcggggucc
cguggaucgccccagccggccggcgccuagcagccgacuuagaacuggug
cggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaaggcc
cgggguguugacgcgaugugauuucugcccagugcucugaaugucaaagu
gaagaaauucaaugaagcgcggguaaacggcgggaguaacuaugacucuc
uuaagguagccaaaugccucgucaugugacgcgcaugaauggaugaacga
gauucccacugucccuaccuacuauccagcgaaaccacagccaagggaac
gggcuuggcggaaucagcggggaaagaagacccuguugagcuugacucua
gucuggcacggugaagagacaugagagguguagaauaagugggaggcggc
cgccggugaaauaccacuacucugaucguuuuuucacugacccggugagg
cggggggcuucuggcgccaagcgcccggccgcgcgccggccgggcgcgac
ccgcuccggggacagugccagguggggaguuugguacaccugucaaacgg
uaacgcagguguccuaaggcgagcucagggaggacagaaaccucccgugg
agcagaagggcaaaagcucgcuugaucuugauuuuguacgaauacagacc
gugaaagcggggccucacccuucugaccuuuuggguuuuaagcaggagga
aguuaccacagggauaacuggcuuguggcggccaagcgagcgacgucgcu
uuuugauccuucgaugucggcucuuccuaucauugugaagcagaauucac
caagcguuggauuguucacccacuaauagggaacgugagcuggguuuaga
ccgucgugagacagguuaguuuuacccuacugaugauguguuguugccau
gguaauccugcucaguacgagaggaaccgcagguucagacauuuggugua
ugugcuuggcugaggagccaauggggcgaagcuaccaucugugggauuau
gacugaacgccucuaagucagaaucccgcccaggcggaacgauagcgccg
cggagccucgguuggccucggauagccgguccccgggguccggugcggag
ugcccuucguccugggaaacggggcgcggccggagaggcggccgcccccu
cgcccgucacgcaccgcacguucguggggaaccuggcgcuaaaccauucg
uagacgaccugcuucugggucgggguuucguacguagcagagcagcuccc
ucgcugcgaucuauugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8fl3 Principles of human pre-60 S biogenesis.
• Resolution: 2.53 Å
• Binding residue (original residue number in PDB): R34 F37 R47 Y51 H58 K59 R62 Y65 R66 I69 R70 M71 R73 M74 R76 R96 G97 I98 N99 P103 K107 L111 Q116 I117 K124 A128 N131 L147 N151 R157 K165 R166 E188 K202 N206 K212 L213 S214 S215 P216 R217 G218 G219 M220 K223 R242 R245
• Binding residue (residue number reindexed from 1): R11 F14 R24 Y28 H35 K36 R39 Y42 R43 I46 R47 M48 R50 M51 R53 R73 G74 I75 N76 P80 K84 L88 Q93 I94 K101 A105 N108 L124 N128 R134 K142 R143 E165 K179 N183 K189 L190 S191 S192 P193 R194 G195 G196 M197 K200 R219 R222

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:8fl3, PDBe:8fl3, PDBj:8fl3
• PDBsum: 8fl3
• PubMed: 37410842
• UniProt: P18124|RL7_HUMAN Large ribosomal subunit protein uL30 (Gene Name=RPL7)