Structure of PDB 8xxn Chain SF Binding Site BS01

Receptor Information

>8xxn Chain SF (length=189) Species: 9606 (Homo sapiens)

DIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKRFRKAQ
CPIVERLTNSMMMHGRNNGKKLMTVRIVKHAFEIIHLLTGENPLQVLVNA
IINSGPREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRN
IKTIAECLADELINAAKGSSNSYAIKKKDELERVAKSNR

Ligand information

>8xxn 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: 8xxn Human tumor suppressor PDCD4 directly interacts with ribosomes to repress translation.
• Resolution: 3.6 Å
• Binding residue (original residue number in PDB): H51 A57 A58 R60 R71 N74 M76 M77 H79 R81 N82 N83 G84 L87 M88 I92 N148 W152 R159 F163 R164 I166 I169
• Binding residue (residue number reindexed from 1): H36 A42 A43 R45 R56 N59 M61 M62 H64 R66 N67 N68 G69 L72 M73 I77 N133 W137 R144 F148 R149 I151 I154

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding

Biological Process

• GO:0000028 ribosomal small subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0006413 translational initiation
• GO:0006450 regulation of translational fidelity
• 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: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:8xxn, PDBe:8xxn, PDBj:8xxn
• PDBsum: 8xxn
• PubMed: 38641729
• UniProt: P46782|RS5_HUMAN Small ribosomal subunit protein uS7 (Gene Name=RPS5)