Structure of PDB 7oya Chain I1 Binding Site BS01

Receptor Information

>7oya Chain I1 (length=201) Species: 7955 (Danio rerio)

RRPARCYRYCKNKPYPKSRFCRGVPDPKIRIFDLGRKKAKVDEFPLCAHM
VSDEYEQLSSEALEAARICANKYMVKTCGKDGFHIRVRLHPFHVIRINKM
LGMRGAFGKPQGTVARVHIGQVIMSVRTKAQNKEHVIEALRRAKFKFPGR
QKIHVSKKYGFTKFNTCDFDNMLAEKRLIPDGCGVKYIPSRGPLSRWKAL
H

Ligand information

>7oya Chain 51 (length=3321)

cacgaccucagcucagacgagaagacccgcugaauuuaagcauauuacua
agcggaggaaaagaaaccaaccgggauucccccaguagcggcgagcgaag
agggaaaaguccagcgccgaauccccgccccagggcgagggaccuguggc
guacggagggccgccucucucggcgcgggggccaaaguccuucugaugga
ggcuuagcccgcggacggugugaggccggugucggcccccgccccgccgg
ggugcgguuccucccggagucggguuguuugggaaugcagcccaaagcgg
gugguaaacuccaucuaaggcuaaauaccggcacgagaccgauagcggac
aaguaccgugagggaaaguugaaaagaacuuugaagagagaguucaacag
ggcgugaaaccguuaagagguaaacggguggggaccgcaccguccgcccg
guggauucagcccggcggggcggggucggcccguccgguggcucccuucg
cucccgcgggggguugacgcccgggcgaaggcucggccgccgccgggugc
auuuccgccgcgguggagcgccgcgaccggcuccgguucggcuuggaagg
gucagggggcgaagguuuuacagcgcccucccgccccgacuucgccgcuu
gcucuccggggccgcgggcccucucugcccucccucugcggggacggggu
cccccgcccccggcguggcgcgacagggguggacuguccucaguccgcug
cgccgcgccgcccagggcgggggacccacguucgggcgcccgagguccgc
ggcgacgccggccucccacccgacccgucuugaaacacggaccaaggagu
ccaacgcgcgcgcgagucagaggguggcucgcgagccccugcggcgcaau
gaaggugagggugggauccccccgccccggcggggggcgcaccaccggcc
cgccucgcgacccuccggggggcagguggaguuggagcgcgcgcgauggc
acccgaaagauggugaacuaugccugggcagggcgaagccaggggaaacu
cugguggaggcccgccgcgguccugacgugcaaaucggucguccgaccug
ggcauaggggcgaaagacuaaucgaaccaucuaguagcugguucccuccg
aaguuucccucaggauagcuggcgcucgccgaucaagcaguuuuauccgg
uaaagccaaugacuagaggcaccuauucucaaacuuuaaauggguaagag
gcccggcucgcuggcgcuggagccgggcguggaaugcgacgcgccuagug
ggccauuuuugguaagcagaacuggugcugcgggaugaaccgaacgccgg
guuaaggcgcccgaugccgacgcucaucagaccccauaaaagguguuggu
ugauauagacagcccgaaucaacuagcccugaaaauggauggcgcuggag
cgucgggcccauacccggccgucgacggcagcugcaagccucgacgagua
ggagggccgccgcgguggcgccgaagcccagggcgcgggcccggguggag
ccgccgcgggcgcagaucuuggugguaguagcaaauauucaaacgagagc
uuugaaggccgaaguggagaaggguuccaugugaacagcaguugaacaug
ggugagccgguccuaagggacgggccuacgccguucggaggggagggccc
cgcucgaccgaaagggagucggguccagauccccgagcccggagcggcgg
agacgggcgccgcgaggcgcccagugcggugacgcaaacgaacccggaga
ugccggcgggugccccgggaaagaguucucuuuucuuugugaagggcagg
gcgcccuggaacggguucgccccgagagaggggcccgcgcccuggaaagc
gccgcgcuucuggcggcguccggugagcucucgucggcccuugaaaaucc
gggggagaagguguaaaucucgcgccgggccguacccauauccgcagcag
gucuccaaggugaacagccucuggcguguuggaacaaggcagaguaaggg
aagucggcaagucagauccguaacuucgggauaaggauuggcucuaaggg
cugauagcagccagcuuagaacugucgcggaccaggggaauccgacuguu
uaauuaaaacaaagcaucgcgaaggcccucggcggguguugacgcgaugu
gauuucugcccagugcucugaaugucaaagugaagaaauucaacgaagcg
cggguaaacggcgggaguaacuaugacucucuuaagguagccaaaugccu
cgucaucuaauuagugacgcgcaugaauggaugaacgagauucccacugu
cccuaccugcuaucuagcgaaaccacagccaagggaacgggcuuggcaga
aucagcggggaaagaagacccuguugagcuugacucuagucuggcccugu
gaagagacuuuccucacuuacccggugaggcgggcuucuggcgucaagcg
ccccgcggggcgcgacccgccccggggacagcgucagguggggaguuuga
cuggggcgguacaccugucaaacgguaacgcagguguccuaaggcgagcu
caggggggacagaaaccucccguagagcagaagggcaaaagcucgcuuga
ucuugauuuucaguaugaguacggaccgcgaaagcggggccucacgaucc
uuccggcuuuugggguuuuaagcgggaggugucagaaaaguuaccacagg
gauaacuggcuuguggcggccaagcguucauagcgacgucgcuuuuugau
ccuucgaugucggcucuuccuaucauugugaagcagaauucaccaagcgu
uggauuguucacccacuaacagggaacgugagcuggguuuagaccgucgu
gagacagguuaguuuuacccuacugaugugagccguuguugcaauaguaa
ucccgcucaguacgagaggaaccgcggguucagacauuugguucgugcgc
uuggcugaggagccacuggcgcgaagccaccaucugcgggauuaugacug
aacgccucuaagucagaaucccgccuaaaagcaacgauaagcgccgucgg
aucuccgauaggccccggguaaccgggaccccggcgcggagagccauucg
ugacaggagcggcuagaacgagcgccgcccccucuuccagugacgcaccg
cauguuuguggggaacccggugcuuaaaugacucguagacgaccugauuc
ugggucggggugucgugcguggcagagcagcgcugcgauccauugaaagu
cagcccucgauccaaguuuug

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7oya A molecular network of conserved factors keeps ribosomes dormant in the egg.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): R3 R4 A6 R7 C8 Y9 K13 N14 K15 P16 F22 D35 K39 E63 A64 A67 K74 R90 H92 F94 R98 N100 L103 G114 M115 R116 G117 A118 F119 Q133 R154 F157 K158 P160 R162 G194 K198
• Binding residue (residue number reindexed from 1): R1 R2 A4 R5 C6 Y7 K11 N12 K13 P14 F20 D33 K37 E61 A62 A65 K72 R88 H90 F92 R96 N98 L101 G102 M103 R104 G105 A106 F107 Q121 R142 F145 K146 P148 R150 G182 K186

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0045182 translation regulator activity

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0006412 translation
• GO:0006417 regulation of translation
• GO:0007420 brain development
• GO:1990403 embryonic brain development

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7oya, PDBe:7oya, PDBj:7oya
• PDBsum: 7oya
• PubMed: 36653451
• UniProt: Q7ZV96|RL10_DANRE Large ribosomal subunit protein uL16 (Gene Name=rpl10)