Structure of PDB 8xxl Chain SM Binding Site BS01

Receptor Information

>8xxl Chain SM (length=122) Species: 9606 (Homo sapiens)

VMDVNTALQEVLKTALIHDGLARGIREAAKALDKRQAHLCVLASNCDEPM
YVKLVEALCAEHQINLIKVDDNKKLGEWVGLCKIDREGKPRKVVGCSCVV
VKDYGKESQAKDVIEEYFKCKK

Ligand information

>8xxl Chain S2 (length=1723)

uaccugguugauccugccaguagcauaugcuugucucaaagauuaagcca
ugcaugucuaaguacgcacggccgguacagugaaacugcgaauggcucau
uaaaucaguuaugguuccuuuggucgcucgcuccucucccacuuggauaa
cugugguaauucuagagcuaauacaugccgacgggcgcugacccccuucg
cgggggggaugcgugcauuuaucaguggugacucuagauaaccucgggcc
gaucgcacgccccccguggcggcgacgacccauucgaacgucugcccuau
caacuuucgaugguagucgccgugccuaccauggugaccacgggugacgg
ggaaucaggguucgauuccggagagggagccugagaaacggcuaccacau
ccaaggaaggcagcaggcgcgcaaauuacccacucccgacccggggaggu
agugacgaaaaauaacaauacaggacucuuucgaggcccuguaauuggaa
ugaguccacuuuaaauccuuuaacgaggauccauuggagggcaagucugg
ugccagcagccgcgguaauuccagcuccaauagcguauauuaaaguugcu
gcaguuaaaaagcucguaguuggaucuuggcucucggccggggcccgaag
cguuuacuuugaaaaaauuagaguguucaaagcaggcccgagccgccugg
auaccgcagcuaggaauaauggaauaggaccgcgguucuauuuuguuggu
uuucggaacugaggccaugauuaagagggacggccgggggcauucguauu
gcgccgcuagaggugaaauucuuggaccggcgcaagacggaccagagcga
aagcauuugccaagaauguuuucauuaaucaagaacgaaagucggagguu
cgaagacgaucagauaccgucguaguuccgaccauaaacgaugccgaccg
gcgaugcggcggcguuauucccaugacccgccgggcagcuuccgggaaac
caaagucuuuggguuccggggggaguaugguugcaaagcugaaacuuaaa
ggaauugacggaagggcaccaccaggaguggagccugcggcuuaauuuga
cucaacacgggaaaccucacccggcccggacacggacaggauugacagau
ugauagcucuuucucgauuccgugggugguggugcauggccguucuuagu
ugguggagcgauuugucugguuaauuccgauaacgaacgagacucuggca
ugcuaacuaguuacgcgacccccgagcggucggcgucccccaacuucuua
gagggacaaguggcguucagccacccgagauugagcaauaacaggucugu
gaugcccuuagauguccggggcugcacgcgcgcuacacugacuggcucag
cgugugccuacccuacgccggcaggcgcggguaacccguugaaccccauu
cgugauggggaucggggauugcaauuauuccccaugaacgaggaauuccc
aguaagugcgggucauaagcuugcguugauuaagucccugcccuuuguac
acaccgcccgucgcuacuaccgauuggaugguuuagugaggcccucggau
cggccccgccggggucggcccacggcccuggcggagcgcugagaagacgg
ucgaacuugacuaucuagaggaaguaaaagucguaacaagguuuccguag
gugaaccugcggaaggaucauua

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8xxl Human tumor suppressor PDCD4 directly interacts with ribosomes to repress translation.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): R33 G34 I35 R36 E37 D57 E58 Y61 N82 L91 V104 C106 S107
• Binding residue (residue number reindexed from 1): R23 G24 I25 R26 E27 D47 E48 Y51 N72 L81 V94 C96 S97

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042274 ribosomal small subunit biogenesis
• GO:0090263 positive regulation of canonical Wnt signaling pathway
• GO:1990145 maintenance of translational fidelity

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005794 Golgi apparatus
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0016020 membrane
• GO:0022626 cytosolic ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0032040 small-subunit processome
• GO:0043231 intracellular membrane-bounded organelle
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8xxl, PDBe:8xxl, PDBj:8xxl
• PDBsum: 8xxl
• PubMed: 38641729
• UniProt: P25398|RS12_HUMAN Small ribosomal subunit protein eS12 (Gene Name=RPS12)