Structure of PDB 8xxn Chain 3B Binding Site BS01

Receptor Information

>8xxn Chain 3B (length=536) Species: 9606 (Homo sapiens)

ADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKT
KGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLDLGNLRYWLEEAEC
RDQYSVIFESGDRTSIFWNDVKDPVSIEERARWTETYVRWSPKGTYLATF
HQRGIALWGGEKFKQIQRFSHQGVQLIDFSPCERYLVTFSPLMDTQDDPQ
AIIIWDILTGHKKRGFHCESSAHWPFKWSHDGKFFARMTLDTLSIYETPS
MGLLDKKSLKISGIKDFSWSPGGNIIAFWVPEDKDIPARVTLMQLPTRQE
IRVRNLFNVVDCKLHWQKNGDYLCVKVDRTPKGTQGVVTNFEIFRMREKQ
VPVDVVEMKETIIAFAWEPNGSKFAVLHGEAPRISVSFYHVKNNGKIELI
KMFDKQQANTIFWSPQGQFVVLAGLRSMNGALAFVDTSDCTVMNIAEHYM
ASDVEWDPTGRYVVTSVSWWSHKVDNAYWLWTFQGRLLQKNNKDRFCQLL
WRPRPPTLLSQEQIKQIKKKIFEQKDRLSQSKASKE

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): K487 D488 K535 G536 Q538
• Binding residue (residue number reindexed from 1): K284 D285 K332 G333 Q335

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003723 RNA binding
• GO:0003743 translation initiation factor activity
• GO:0005515 protein binding
• GO:0031369 translation initiation factor binding
• GO:0060090 molecular adaptor activity

Biological Process

• GO:0001732 formation of cytoplasmic translation initiation complex
• GO:0002183 cytoplasmic translational initiation
• GO:0006412 translation
• GO:0006413 translational initiation
• GO:0006446 regulation of translational initiation
• GO:0075522 IRES-dependent viral translational initiation
• GO:0075525 viral translational termination-reinitiation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005852 eukaryotic translation initiation factor 3 complex
• GO:0010494 cytoplasmic stress granule
• GO:0016282 eukaryotic 43S preinitiation complex
• GO:0033290 eukaryotic 48S preinitiation complex
• GO:0045202 synapse
• GO:0070062 extracellular exosome
• GO:0071541 eukaryotic translation initiation factor 3 complex, eIF3m

External links

• PDB: RCSB:8xxn, PDBe:8xxn, PDBj:8xxn
• PDBsum: 8xxn
• PubMed: 38641729
• UniProt: P55884|EIF3B_HUMAN Eukaryotic translation initiation factor 3 subunit B (Gene Name=EIF3B)