Structure of PDB 8xxm Chain SO Binding Site BS01

Receptor Information

>8xxm Chain SO (length=140) Species: 9606 (Homo sapiens)

EQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGKETICRVTGGMK
VKADRDESSPYAAMLAAQDVAQRCKELGITALHIKLRATGGNRTKTPGPG
AQSALRALARSGMKIGRIEDVTPIPSDSTRRKGGRRGRRL

Ligand information

>8xxm 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: 8xxm Human tumor suppressor PDCD4 directly interacts with ribosomes to repress translation.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): N38 D39 F41 H43 G49 K50 T52 R55 T57 G59 M60 D65 R66 R98 R104 I135 P136 S137 D138 S139 T140 R141 K143 G144 G145 R146 R147 R149 R150
• Binding residue (residue number reindexed from 1): N27 D28 F30 H32 G38 K39 T41 R44 T46 G48 M49 D54 R55 R87 R93 I124 P125 S126 D127 S128 T129 R130 K132 G133 G134 R135 R136 R138 R139

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0045182 translation regulator activity
• GO:0048027 mRNA 5'-UTR binding

Biological Process

• GO:0000028 ribosomal small subunit assembly
• GO:0000122 negative regulation of transcription by RNA polymerase II
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0006417 regulation of translation
• GO:0030218 erythrocyte differentiation
• GO:0030490 maturation of SSU-rRNA
• GO:0042274 ribosomal small subunit biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0014069 postsynaptic density
• GO:0015935 small ribosomal subunit
• GO:0016020 membrane
• GO:0022626 cytosolic ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0032040 small-subunit processome
• GO:0045202 synapse
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8xxm, PDBe:8xxm, PDBj:8xxm
• PDBsum: 8xxm
• PubMed: 38641729
• UniProt: P62263|RS14_HUMAN Small ribosomal subunit protein uS11 (Gene Name=RPS14)