Structure of PDB 7oyc Chain 11 Binding Site BS01

Receptor Information

>7oyc Chain 11 (length=136) Species: 8355 (Xenopus laevis)

SGDAGASSTFPMQCSALRKNGFVVLKGRPCKIVEMSTSKTGKHGHAKVHM
VGIDIFSGKKYEDICPSTHNMDVPNIKRCDYQLIGIIDNYLSLLSDSGDV
REDLKEILAKHEAGEEILVTVLNAMSEECAVALKAM

Ligand information

>7oyc Chain 51 (length=3245)

ucagaccucagaucagacgcggcgacccgcugaauuuaagcauauuacua
agcggaggaaaagaaacuaaccaggauucccccaguaacggcgagugaag
agggaagagcccagcgccgaauccccgcccgcgggcgcgggacguguggc
guacgggagaccggacccccccggcgcgcgggggcccaaguccuucugau
cgaggcccagcccgcggacgguguuaggccgguggcggcccccggcgcgg
cgggacccggucuccucggagucggguuguuugggaaugcagcccaaagc
gggugguaaacuccaucuaaggcuaaauaccggcacgagaccgauagcgg
acaaguaccguaagggaaaguugaaaagaacuuugaagagagaguucaag
agggcgugaaaccguuaagagguaaacgggugggguccgugcgguccgcc
cggaggauucaacccggcggguccgccggccggaccgggccacucggcgg
gacgcggcccgggcggccccggcgcccgcagggcgcauuuccuccgcggc
ggugcgccgcgaccggcuccgggccggcugggaaggcccagggguucagg
ggaguuacagcccccccccaggcagcaucgccgucgcccggggccgaggg
uccgcggccuccuccccaagggggaaggggccccccgcucccggcgcggc
gcggacugcccccagugcgcgccgcgccgccgaggcgggagggcccgcgg
gagccgccagggguccgcggcgaugucggugucccacccgacccgucuug
aaacacggaccaaggagucuaacgcgcgcgcgagucggagggacgcgaaa
cccuguggcgcaaugaaggugagggccggggcgccccggcugagguggga
ucccgccgcgccggcgggcgcaccaccggcccgucucgcccgccccgucg
gggagguggagcgugagcgcgcgcgauaggacccgaaagauggugaacua
ugccugggcagggcgaagccagaggaaacucugguggagguccguagcgg
uccugacgugcaaaucggucguccgaccuggguauaggggcgaaagacua
aucgaaccaucuaguagcugguucccuccgaaguuucccucaggauagcu
ggcgcucguccgucgcaguuuuauccgguaaagcgaaugauuagagguac
cuauucucaaacuuuaaauggguaagaagcccggcucgcuggcuuggagc
cgggcguggaaugcgagcacgccuagugggccacuuuugguaagcagaac
uggcgcugcgggaugaaccgaacgccggguuaaggcgcccgaugccgacg
cucaucagaccccagaaaagguguugguugauauagacagcgccgaauca
acuagcccugaaaauggauggcgcuggagcgucgggcccauacccggccg
ucgccggcgcugggcuaggccgcgacgaguaggagggccgccgcgguggg
cgcggaagccccgggcgagggcccggguggagccgccgcgggugcagauc
uuggugguaguagcaaauauucaaacgagaacuuugaaggccgaagugga
gaaggguuccaugugaacagcaguugaacaugggucagucgguccuaaga
gaugggcgagcgccguucggaagggcggccgaucgaaagggagucggguu
cagauccccgaacccggagcggagacgggcguccagugcggcgacgcgac
cgaucccggagaagccggcgggagccccggggagaguucucuuuucuuug
ugaagggcagggccgcccuggaauggguucgccccgagagaggggcccgc
gccuuggaaagcgucgcgggcggcguccggugagcucucgcuggcccuug
aaaauccgggggagaggguguaaaucucgcgccgggccguacccauaucc
gcagcaggucuccaaggugaacagccucuggcauguuagaacaauguagg
uaagggaagucggcaagucagauccguaacuucgggauaaggauuggcuc
uaagggcuggcagcugacuuagaacuggugcggaccaggggaauccgacu
guuuaauuaaaacaaagcaucgcgaaggcccgaggcggguguugacgcga
ugugauuucugcccagugcucugagucaaagugaagaaauucaaugaagc
gcggguaaacggcaagguagccaaaugccucgucaucuaauuagugacgc
gcaugaauggaugaacgagauucccacugucccuaccuacuaucuagcga
aaccacagccaagggaacgggcuuggcggaaucagcggggaaagaagacc
cuguugagcuugacucuagucugcaacugugaaguuucacuuacccggug
aggcggggggcuucuggacccaagcgcccggcgggcgcgacccgcuccga
ggacaguggcagguggggaguuugacuggggcgguacaccugucaaaccg
uaacgcagguguccuaaggcgagcucagggaggacagaaaccucccgugg
agcagaagggcaaaagcucgcuugaucuugauuuucaguaugaauacaga
ccgugaaagcggggccucacgauccuucugacuuuuuggguuuuaagcag
gaggugucagaaaaguuaccacagggauaacuggcuuguggcggccaagc
guucauagcgacgucgcuuuuugauccuucgaugucggcucuuccuauca
uugugaagcagaauucaccaagcguuggauuguucacccacuaauaggga
acgugagcuggguuuagaccgucgugagacagguuaguuuuacccuacug
augauguguugucgcaauaguaauccugcucaguacgagaggaaccgcag
guucagacauuugguguaugugcuuggcugaggagccaauggggcgaagc
uaccaucugugggauuaugacugaacgccucuaagucagaauccccccua
aacgugacgauaagcgccgcggagccucggucggccucggauagccggcg
cgccggcgggcagagccgcucgccucgggaccggagcgcggacgaaaggg
ggccgccucucucccggagcgcaccgcacguucguggggaaccuggugcu
aaaucauucguagacgaccugauucugggucaggguuucgugcguagcag
agcagcgcugcgaucuauugaaagucaucccuugagccauuuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7oyc A molecular network of conserved factors keeps ribosomes dormant in the egg.
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): S47 T49 G50 X51 H52 G53 H54 A55 K56 K68 K69 E71 D72 I73 S76
• Binding residue (residue number reindexed from 1): S38 T40 G41 X42 H43 G44 H45 A46 K47 K59 K60 E62 D63 I64 S67

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003743 translation initiation factor activity
• GO:0003746 translation elongation factor activity
• GO:0005515 protein binding
• GO:0043022 ribosome binding

Biological Process

• GO:0006412 translation
• GO:0006413 translational initiation
• GO:0006414 translational elongation
• GO:0045901 positive regulation of translational elongation
• GO:0045905 positive regulation of translational termination

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005789 endoplasmic reticulum membrane
• GO:0016020 membrane

External links

• PDB: RCSB:7oyc, PDBe:7oyc, PDBj:7oyc
• PDBsum: 7oyc
• PubMed: 36653451
• UniProt: Q7ZXG3|IF5A1_XENLA Eukaryotic translation initiation factor 5A-1 (Gene Name=eif5a.L)