Structure of PDB 6z6m Chain LW Binding Site BS01

Receptor Information

>6z6m Chain LW (length=118) Species: 9606 (Homo sapiens)

MKVELCSFSGYKIYPGHGRRYARTDGKVFQFLNAKCESAFLSKRNPRQIN
WTVLYRRKHKKGQKRTRRAVKFQRAITGASLADIMAKRNQKPEVRKAQRE
QAIRAAKEAKKAKQASKK

Ligand information

>6z6m Chain L5 (length=3772)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgg
cccggcggaucuuucccgcgcgggggaccgucccccgaccggcgaccggc
cgccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccggg
acggcugggaaggcccggcggggaagguggcucgggggcccccgaguguu
acagcccccccggcagcagcacucgccgaaucccggggccgagggagcga
gacccgucgccgcgcucuccccccucccggcgcgccggggggggccgggc
caccccucccacggcgcgaccgcucggggcggacuguccccagugcgccc
cgggcgggucgcgccgucgggcccgggggaggccacgcgcgcgucccccg
aagagggggacggcggagcgagcgcacggggucggcggcgacgucggcua
cccacccgacccgucuugaaacacggaccaaggagucuaacacgugcgcg
agucgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggccg
gcgcgcucgccggccgaggugggaucccgaggccucuccaguccgccgag
ggcgcaccaccggcccgucucgcccgccgcgccggggagguggagcacga
gcgcacguguuaggacccgaaagauggugaacuaugccugggcagggcga
agccagaggaaacucugguggagguccguagcgguccugacgugcaaauc
ggucguccgaccuggguauaggggcgaaagacuaaucgaaccaucuagua
gcugguucccuccgaaguuucccucaggauagcuggcgcucucgcagacc
cgacgcccgccacgcaguuuuauccgguaaagcgaaugauuagaggucuu
ggggccgaaacgaucucaaccuauucucaaacuuuaaauggguaagaagc
ccggcucgcuggcguggagccgggcguggaaugcgagugccuagugggcc
acuuuugguaagcagaacuggcgcugcgggaugaaccgaacgccggguua
aggcgcccgaugccgacgcucaucagaccccagaaaagguguugguugau
auagacagcaggacgguggccauggaagucggaauccgcuaaggagugug
uaacaacucaccugccgaaucaacuagcccugaaaauggauggcgcugga
gcgucgggcccauacccggccgucgccggcagucgagaguggacgggagc
ggcggccggagccccgcggacgcuacgccgcgacgaguaggagggccgcu
gcggugagccuugaagccuagggcgcgggcccggguggagccgccgcagg
ugcagaucuuggugguaguagcaaauauucaaacgagaacuuugaaggcc
gaaguggagaaggguuccaugugaacagcaguugaacaugggucagucgg
uccugagagaugggcgagcgccguuccgaagggacgggcgauggccuccg
uugcccucggccgaucgaaagggagucggguucagauccccgaauccgga
guggcggagaugggcgccgcgaggcguccagugcgguaacgcgaccgauc
ccggagaagccggcgggagccccggggagaguucucuuuucuuugugaag
ggcagggcgcccuggaauggguucgccccgagagaggggcccgugccuug
gaaagcgucgcgguuccggcggcguccggugagcucucgcuggcccuuga
aaauccgggggagaggguguaaaucucgcgccgggccguacccauauccg
cagcaggucuccaaggugaacagccucuggcauguuggaacaauguaggu
aagggaagucggcaagccggauccguaacuucgggauaaggauuggcucu
aagggcugggucggucgcggccggcgccuagcagccgacuuagaacuggu
gcggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaaggc
ccgcggcggguguugacgcgaugugauuucugcccagugcucugaauguc
aaagugaagaaauucaaugaagcgcggguaaacggcgggaguaacuauga
cucucuuaagguagccaaaugccucgucaucuaauuagugacgcgcauga
auggaugaacgagauucccacugucccuaccuacuauccagcgaaaccac
agccaagggaacgggcuuggcggaaucagcggggaaagaagacccuguug
agcuugacucuagucuggcacggugaagagacaugagagguguagaauaa
gugggaggcccccggcgcccccccgguguccccgcgaggggcccggggcg
ggguccgccggcccugcgggccgccggugaaauaccacuacucugaucgu
uuuuucacugacccggugaggcgggggggcgagccccgaggggcucucgc
uucuggcgccaagcgcccggccgcgcgccggccgggcgcgacccgcuccg
gggacagugccagguggggaguuugacuggggcgguacaccugucaaacg
guaacgcagguguccuaaggcgagcucagggaggacagaaaccucccgug
gagcagaagggcaaaagcucgcuugaucuugauuuucaguacgaauacag
accgugaaagcggggccucacgauccuucugaccuuuuggguuuuaagca
ggaggugucagaaaaguuaccacagggauaacuggcuuguggcggccaag
cguucauagcgacgucgcuuuuugauccuucgaugucggcucuuccuauc
auugugaagcagaauucaccaagcguuggauuguucacccacuaauaggg
aacgugagcuggguuuagaccgucgugagacagguuaguuuuacccuacu
gaugauguguuguugccaugguaauccugcucaguacgagaggaaccgca
gguucagacauuugguguaugugcuuggcugaggagccaauggggcgaag
cuaccaucugugggauuaugacugaacgccucuaagucagaaucccgccc
aggcggaacgauacggcagcgccgcggagccucgguuggccucggauagc
cggucccccgccgggguccggugcggagugcccuucguccugggaaacgg
ggcgcggccggagaggcggccgcccccucgcccgucacgcaccgcacguu
cguggggaaccuggcgcuaaaccauucguagacgaccugcuucugggucg
ggguuucguacguagcagagcagcucccucgcugcgaucuauugaaaguc
agcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6z6m Structure and function of yeast Lso2 and human CCDC124 bound to hibernating ribosomes.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): K35 R44 Q48 I49 N50 W51 R56 K61
• Binding residue (residue number reindexed from 1): K35 R44 Q48 I49 N50 W51 R56 K61

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0045296 cadherin binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0010458 exit from mitosis
• GO:0021554 optic nerve development
• GO:0031290 retinal ganglion cell axon guidance
• GO:0060041 retina development in camera-type eye

Cellular Component

• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6z6m, PDBe:6z6m, PDBj:6z6m
• PDBsum: 6z6m
• PubMed: 32687489
• UniProt: P83731|RL24_HUMAN Large ribosomal subunit protein eL24 (Gene Name=RPL24)