Structure of PDB 7ls1 Chain S2 Binding Site BS01

Receptor Information

>7ls1 Chain S2 (length=134) Species: 10090 (Mus musculus)

MKFNPFVTSDRSKNRKRHFNAPSHIRRKIMSSPLSKELRQKYNVRSMPIR
KDDEVQVVRGHYKGQQIGKVVQVYRKKYVIYIERVQREKANGTTVHVGIH
PSKVVITRLKLDKDRKKILERKAKSRQVGKEKGK

Ligand information

>7ls1 Chain A2 (length=3707)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggaaaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccgcgcgucgcggcgugggaaau
guggcguacggaagacccacuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcucgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcgcguccggccgugccggugg
uccggcggaucuuucccgcgcgggggaccgcccccggccggcgaccggcc
gccgccgggcgcacuuccaccguggcggugcgccgcgaccggcuccggga
cggccgggaaggcccgguggggaagguggcucggggggggcucaccccga
guguuacagcccuccggccgcgcuuuucgccgaaucccggggccgaggaa
gcccgucgccgcgcucucccucucccgggugggggccgggccgccccucc
cacggcgcgaccgcucggggcggacuguccccagugcgccccgggcgucg
ucgcgccgucgggucccgggggcgucggucacgcgugacgaagccgagcg
cacggggucggcggcgaugucggcuacccacccgacccgucuugaaacac
ggaccaaggagucuaacgcgugcgcgagucaggggcucguccgaaagccg
ccguggcgcaaugaaggugaagggccccgcccgggggcccgaggugggau
cccgaggccucuccaguccgccgagggcgcaccaccggcccgucucgccc
gccgcgccggggagguggagcacgagcguacgcguuaggacccgaaagau
ggugaacuaugcuugggcagggcgaagccagaggaaacucugguggaggu
ccguagcgguccugacgugcaaaucggucguccgaccuggguauaggggc
gaaagacuaaucgaaccaucuaguagcugguucccuccgaaguuucccuc
aggauagcuggcgcucucgcuacgcaguuuuauccgguaaagcgaaugau
uagaggucuuggggccgaaacgaucucaaccuauucucaaacuuuaaaug
gguaagaagcccggcucgcuggcguggagccgggcguggaaugcgagugc
cuagugggccacuuuugguaagcagaacuggcgcugcgggaugaaccgaa
cgccggguuaaggcgcccgaugccgacgcucaucagaccccagaaaaggu
guugguugauauagacagcaggacgguggccauggaagucggaauccgcu
aaggaguguguaacaacucaccugccgaaucaacuagcccugaaaaugga
uggcgcuggagcgucgggcccauacccggccgucgccggcagucggaacg
gaacgggacgggagcggcgucgggccccgcggagccuacgccgcgacgag
uaggagggccgcugcggugagccuugaagccuagggcgcgggcccgggug
gagccgccgcaggugcagaucuuggugguaguagcaaauauucaaacgag
aacuuugaaggccgaaguggagaaggguuccaugugaacagcaguugaac
augggucagucgguccugagagaugggcgagugccguuccgaagggacgg
gcgauggccuccguugcccucggccgaucgaaagggagucggguucagau
ccccgaauccggaguggcggagaugggcgccgcgaggcguccagugcggu
aacgcgaccgaucccggagaagccggcgggagccucggggagaguucucu
uuucuuugugaagggcagggcgcccuggaauggguucgccccgagagagg
ggcccgugccuuggaaagcgucgcgguuccggcggcguccggugagcucu
cgcuggcccuugaaaauccgggggagaggguguaaaucucgcgccgggcc
guacccauauccgcagcaggucuccaaggugaacagccucuggcauguug
gaacaauguagguaagggaagucggcaagccggauccguaacuucgggau
aaggauuggcucuaagggcugggucggucgcggccggcgccuagcagccg
acuuagaacuggugcggaccaggggaauccgacuguuuaauuaaaacaaa
gcaucgcgaaggcccgcggcggguguugacgcgaugugauuucugcccag
ugcucugaaugucaaagugaagaaauucaaugaagcgcggguaaacggcg
ggaguaacuaugacucucuuaagguagccaaaugccucgucaucuaauua
gugacgcgcaugaauggaugaacgagauucccacugucccuaccuacuau
ccagcgaaaccacagccaagggaacgggcuuggcggaaucagcggggaaa
gaagacccuguugagcuugacucuagucuggcacggugaagagacaugag
agguguagaauaagugggaggcccggccgccggugaaauaccacuacucu
caucguuuuuucacugacccggugaggcgggggggcgagccccgaggggc
ucucgcuucuggcgccaagcguccgucccgcgcgugcgggcgggcgcgac
ccgcuccggggacagugccagguggggaguuugacuggggcgguacaccu
gucaaacgguaacgcagguguccuaaggcgagcucagggaggacagaaac
cucccguggagcagaagggcaaaagcucgcuugaucuugauuuucaguac
gaauacagaccgugaaagcggggccucacgauccuucugaccuuuugggu
uuuaagcaggaggugucagaaaaguuaccacagggauaacuggcuugugg
cggccaagcguucauagcgacgucgcuuuuugauccuucgaugucggcuc
uuccuaucauugugaagcagaauucaccaagcguuggauuguucacccac
uaauagggaacgugagcuggguuuagaccgucgugagacagguuaguuuu
acccuacugaugauguguuguugccaugguaauccugcucaguacgagag
gaaccgcagguucagacauuugguguaugugcuuggcugaggagccaaug
gggcgaagcuaccaucugugggauuaugacugaacgccucuaagucagaa
ucccgcccaggcggaacgauacggcagcgccgaggagccucgguuggccc
cggauagccggguccccguccugccccgcggccgggcgucgggaccgggg
uccggugcggagagccguucgucuugggaaacggggugcggccggaaagg
gggccgcccucucgcccgucacguugacgcacguucguguggaaccuggc
gcuaaaccauucguagacgaccugcuucugggucgggguuucguacguag
cagagcagcucccucgcugcgaucuauugaaagucagcccucgacacaag
gguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7ls1 Functionally distinct roles for eEF2K in the control of ribosome availability and p-body abundance.
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): M1 K2 F3 N4 T8 S9 D10 R11 K13 R15 R17 H18 K28 I29 S31 P33 R45 S46 R59 G60 H61 K63 K77 R87 K89 A90 H100 S102 K103 R121 K122 S125 R126
• Binding residue (residue number reindexed from 1): M1 K2 F3 N4 T8 S9 D10 R11 K13 R15 R17 H18 K28 I29 S31 P33 R45 S46 R59 G60 H61 K63 K77 R87 K89 A90 H100 S102 K103 R121 K122 S125 R126

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0048027 mRNA 5'-UTR binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0006977 DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest
• GO:0034644 cellular response to UV
• GO:0042273 ribosomal large subunit biogenesis
• GO:0045727 positive regulation of translation
• GO:0071479 cellular response to ionizing radiation
• GO:0071480 cellular response to gamma radiation
• GO:0140236 translation at presynapse
• GO:0140242 translation at postsynapse
• GO:1902164 positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator
• GO:1902167 positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
• GO:1904803 regulation of translation involved in cellular response to UV

Cellular Component

• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:0098793 presynapse
• GO:0098794 postsynapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7ls1, PDBe:7ls1, PDBj:7ls1
• PDBsum: 7ls1
• PubMed: 34815424
• UniProt: P61255|RL26_MOUSE Large ribosomal subunit protein uL24 (Gene Name=Rpl26)