Structure of PDB 8fkz Chain LF Binding Site BS01

Receptor Information

>8fkz Chain LF (length=103) Species: 9606 (Homo sapiens)

QVLKFTLDCTHPVEDGIMDAANFEQFLQERIKVNGKAGNLGGGVVTIERS
KSKITVTSEVPFSKRYLKYLTKKYLKKNNLRDWLRVVANSKESYELRYFQ
INQ

Ligand information

>8fkz Chain L3 (length=2833)

gcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguca
gcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaaca
gggaagagcccagcgccgaauccccgccccggggcgcgggacauguggcg
uacggaagacccgcuccccggcgccgcgggggcccaaguccuucugaucg
aggcccagcccguggacggugugaggccgguagcggcccccggcgcgccg
ggcccgggucuucccggagucggguugcuugggaaugcagcccaaagcgg
gugguaaacuccaucuaaggcuaaauaccggcacgagaccgauagucaac
aaguaccguaagggaaaguugaaaagaacuuugaagagagaguucaagag
ggcgugaaaccguuaagagguaaacgggugggguccgcgcaguccgcccg
gaggauucaacccggcggcggccggccgugucggcggcccggcggaucug
ggaccgucccccgaccggcgaccggccgccgccgggcgcauuuccaccgc
ggcggugcgccgcgaccggcuccgggacggcugggaaggcccggcgggga
agguggcucgggcccgaguguuacagcccccccggcagcagcacucgccg
aaucccggggccgagggagucgccgcgcucuccccccggggggccgggcc
accccucccacggcgcgcgccgucgggcccggggggccacgcgcgcgucc
cccgaagagggggacggcggagcgagcgcacggggucggcggcgacgucg
gcuacccacccgacccgucaaacacggaccaaggagucuaacacgugcgc
gagucgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggcc
gcggccgaggugggaucccgaggccgccgagggcgcaccaccggcccguc
ucgcccgccgcgccggggagguggagcacgagcgcacguguuaggacccg
aaagauggugaacuaugccugggcagggcgaagccagaggaaacucuggu
ggagguccguagcguccgaccuggguauaccaucuaguagcugguucccu
ccgaaguuucccucaggauagcuggcgcucuccgcaguuuuauccggggg
uaagaagcccggcucgcuggcguggagccgggcguggaaugcgagugccu
agugggccacuuuugguaagcagaacuggcgcugcgggaugaaccgaacg
ccggguuaaggcgcccgaugccgacgcucaucagaccagaaaagguguug
guugauauagacagcaggacgguggccauggaagucggaauccgcuaagg
aguguguaacaacucaccugccgaaucaacuagcccugaaaauggauggc
gcuggagcgucgggcccauacccggccgucgccggcagugacgcuacgcc
gcgacgaguaggagggccgcugcggugagccuugaagccuagggcgcggg
cccggguggagccgccgcaggugcagaucuuggugguaguagcaaauauu
caaacgagaacuuugaaggccgaaguggagaaggguuccaugugaacagc
aguugaacaugggucagucgguccugagagaugggcgagcgccguuccga
agggacgggcgauggccuccggcccucgaucgaaagggagucggguucag
auccccgaauccggaguggcggagaugggcgccgcgaggcguccagugcg
guaacgcgaccgaucccggagaagccggcgggagccccggggagaguucu
cuuuucuuugugaagggcagggcgcccuggaauggguucgccccgagaga
ggggcccgugccuuggaaagcgucgcgguuccggcggcguccggugagcu
cucgcuggcccuugaaaauccgggggagaggguguaaaucucgcgccggg
ccguacccauauccgcagcaggucuccaaggugaacagccucuggcaugu
uggaacaauguagguaaggggcucuaagggcugggucggucgggcugggg
cgcgaagcggggucccguggaucgccccagccggccggcgccuagcagcc
gacuuagaacugcaucgcgaaggcccgggguguugacgcgauguuguccc
uaccuacuauccagcgaaaccacagccaagggaacgggcuuggcggaauc
agacccggugaggcggggggcuucuggcgccaagcgcccggccgcgcgcc
ggccgggcgcgacccgcuccggggcuucugaccuuuuggguuuuaagcag
gagggcuuguggcggccaagcgagcgacgucgcuuuuugcggcucuuccu
aucauugugaagcagaauucaccaagcguuggauuguucacccacuaaua
gggaacgugagcuggcuacugaugauguguuguugccaugguaauccugc
ucaguacgagaggaaccgcagguucagacauuugguguaugugcuuggcu
gaggagccaauggggcgaagcuaccaucugugggauuaugacugaacgcc
ucuaagucagaaucccgcccaggcggaacgauagcgccgcggagccucgg
uuggccucggauagccgguccccgggguccggugcggagugcccuucguc
cugggaaacggggcgcggccggagaggcggccgcccccucgcccgucacg
caccgcacguucguggggaaccuggcgcuaaaccauucguagacgaccug
cuucugggucgggguuucguacguagcagagcagcucccucgcugcgauc
uauugaaagucagcccucgacacaaggguuugu

........................<<<<<<.....<<....>>......>
>>>>.>.........<<....>>..<<<<<<.....<<.....>>....>
>>>>>..[[[..<<<<<...<<<<<<<<<..>>>>>.>>>>.....>>>>
>..<<<<<<<<<<...<<<<<<<<.<<<<<<<<<<....<<<<......>
>>>.....((......<<<.....))>>>...>.>>>>>>>.>>>>>>>>
>>..>>>>>>>>>>.......<<<<<<<........>>>>>>>.....((
(((..<<<<<<)))))..]]].............................
.....<<....>>...............<<<......>>>..........
........................<<<<<<<<..<<<.<<...<<<<<<<
<.<<<.....<<<<<<<<<<<<<<<<<<.<<<<<.<<...<<<<<.<<<.
>>>>>>>>>>>>>>>>>>>...>>>>>>>>>>>>>>......>>>.>>>.
>>>>>...<<<<<<<<<<<<<<<<<<<<<<<...<<..<<<.<<.<<<<.
.....<<<<<<..>>>>>>.......>>>>>>.>>>........>>>>>>
..>>>>>>>>>>>...........<<<<<<.<<<<<..>>>>>.<<<<<<
.<<<<.<<<<<<<<<..>>>>>>.>>>...>>>>>>>>.>>..<<<<<<<
<<.......>>>>>>>.>>....>>>>>>.....>>>.>>>>>...>>>>
>...>>>>>>>>..<<<<.....>>>><<<<<<....<<<<<<<<<<<<<
..<<<...<<<<........>>>>.....>>>...<<....>>...<<<<
..>>>>..<<<<<...<<<..<<<.>>>..>>>....>>>>>.<<<<<<<
<<.<<<<......>>>>>>>>>>>.>>....>>>>>>>>>>>>>..<<.<
...<<<<<<.....<<<<<<<<<..<<<....<<<<<<<....>>>>>>>
.....>>>...<..>....>>>>>>>>>>>>>>>......>.>>..<<<<
<<......<<<....>>>..<<.<<<<<<<...<<<.<<<<<<<<..>>>
>>>...<<<<<<<<<.<......>>>>>>>>>>....>>>>>>>>>>>>.
.>>..<<<<.<<<<<.....>>>>>.>>>>....<<<......>>>...<
<<<<<<...<<<(((.......<<<<<.....<<........<<<.<<<<
<<<<<<.......<<<<<.<<<...<<.........>>...>>>......
...<<......>>...>>>>>...>>>>>>>>>>>>>..........)))
.>>...>>>>>..>>>...>>>>>>><<<<<<.<<<...........>>>
>>>>>>....>>>>>>.<.<<<<<<<<.<<......<<<<.<<<<....>
>>>>>>>...>>>>>>>>>>..>.....>>>>>><<.....<<.....<<
<<<<.......>>>>>>.<<<.....<<<<<.<<...<<<<<<...<<..
...>>.>>>>>>....((<<<<<<...<<....<<<....>>>.......
......<<<<...........>>>>....>>....>>>..<<<<<.....
...>>>>>))<<<<....<<<<<..<<<<<<<<....>>>>>>>>..<<<
....>>>...<..<<<<<<<...<<<<<<<<<<<<.<<<<<<<<<<..{{
{..>>>>>>....<<<<<.<<<<.<<<<.....<<<.....>>>.....>
>>>>>>>..>>>>>.....<<<<<<<.......>>>>>>>>>>>...>>>
>>>>>>>>>.........>>>>>>>..>..........>>.>>>.>>>>.
>>>..>>.....<<......>>>>>>>.<<<<.....>>>>..>>>....
<<<<.....<<<<<<<.<<.<.<<<<<<<<<<<.<<<<<<<<.<<<<<<<
<<....<<<<<..>>>>>....>>>>>>>>>>>>>>>>>......>>>>>
..>>>>>>.>.<<<<<<<....<<<<.>>>>......>>>>>>>...>>.
>>>>>>>..>>>>>>....>>....<<<<<........>>>>>....[[[
[[.<<<<<.....<<<<................<<<<<<<<<<.......
>>>>>>>>>>..>>>>..>>>>>.((((((..(((..>>>>>>.))))))
))).......<<<<<<...<<..>>...>>>>>>.....<<<<.<<<<<<
..<.<.<<<<<......>>>>>...>.>.<<<.........>>>.....>
>>>>..>...>>>>....]]]]].....<<<<<<.<..<<<..<.<<<<<
.................>>>>>.><<<<....<<<<....<<.<<<<<<.
}}}..>>>>..>>.>>...>>>>...>>>><<<<<...<<<<<.......
....>>>>>...>>>>>.>>>...>.>>>>>>.<<<<<<.<<..<<<<..
..<<<........<<<<<.<<<<>>>>.>>>>>.......>>>...<<<.
.<<<<....<<<<.<<<<<<<......>>>>>>>>>>>...>>>>..>>>
..............>>>>..>>>>>>>>.<<<<<.<.............>
....<<.<<<<<<<.<<.....<<<<....<<<<<......>>>>>...>
>>>....>>....>>>.>>>>.>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8fkz Principles of human pre-60 S biogenesis.
• Resolution: 3.04 Å
• Binding residue (original residue number in PDB): K48 S79 K80 R81 Y82 K84 Y85 K88 K89 K92 R101 V103 A104 K107 Y110 R113
• Binding residue (residue number reindexed from 1): K32 S63 K64 R65 Y66 K68 Y69 K72 K73 K76 R85 V87 A88 K91 Y94 R97

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0008201 heparin binding
• GO:0042802 identical protein binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0046632 alpha-beta T cell differentiation
• GO:0140236 translation at presynapse

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:0070062 extracellular exosome
• GO:0098793 presynapse
• GO:0098978 glutamatergic synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8fkz, PDBe:8fkz, PDBj:8fkz
• PDBsum: 8fkz
• PubMed: 37410842
• UniProt: P35268|RL22_HUMAN Large ribosomal subunit protein eL22 (Gene Name=RPL22)