Structure of PDB 7oyb Chain A1 Binding Site BS01

Receptor Information

>7oyb Chain A1 (length=245) Species: 7955 (Danio rerio)

GRVIRGQRKGAGSVFKAHVKHRKGAAKLRHIDFAERHGYIKGIVKDIIHD
PGRGAPLAKVMFRDPYRFKKRTELFIAAEGIHTGQFIYCGKKAQLNIGNV
LPVGTMPEGTIVCCLEEKPGDRGKLARASGNYATVISHNPETKKSRVKLP
SGSKKVISSANRAVVGVVAGGGRIDKPILKAGRAYHKYKAKRNCWPRVRG
VAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAARRTGRL

Ligand information

>7oyb Chain 51 (length=3263)

cacgaccucagcucagacgagaagacccgcugaauuuaagcauauuacua
agcggaggaaaagaaaccaaccgggauucccccaguagcggcgagcgaag
agggaaaaguccagcgccgaauccccgccccagggcgagggaccuguggc
guacggagggccgccucucucggcgcgggggccaaaguccuucugaugga
ggcuuagcccgcggacggugugaggccggugucggcccccgccccgccgg
ggugcgguuccucccggagucggguuguuugggaaugcagcccaaagcgg
gugguaaacuccaucuaaggcuaaauaccggcacgagaccgauagcggac
aaguaccgugagggaaaguugaaaagaacuuugaagagagaguucaacag
ggcgugaaaccguuaagagguaaacggguggggaccgcccgcccggugga
uucagcccggcggggcggggucggcccguccgguggcucccuucgcgggg
uugacgcccgggcgaaggcucggccgccgccgggugcauuuccgccgcgg
uggagcgccgcgaccggcuccgguucggcuuggaagggucagggggcgaa
gguuuuacagcgcccucccgccccgacgccgcuugcucuccggggccgcg
ggcccucucugcccucccucugcggggacggggucccccgcccccggcgu
ggcgcgacagggguggacuguccucaguccgcugcgccgcgccgcgggcg
ggggacccacguucgggcgcccgagguccgcggcgacgccggccucccac
ccgacccgucuugaaacacggaccaaggaguccaacgcgcgcgcgaguca
gaggguggcucgcgagccccugcggcgcaaugaaggugagggugggaucc
ccccgccccggcggggggcgcaccaccggcccgccucgcgacccuccggg
gggcagguggaguuggagcgcgcgcgauggcacccgaaagauggugaacu
augccugggcagggcgaagccaggggaaacucugguggaggcccgccgcg
guccugacgugcaaaucggucguccgaccugggcauaggggcgaaagacu
aaucgaaccaucuaguagcugguucccuccgaaguuucccucaggauagc
uggcgcucgccgaucaagcaguuuuauccgguaaagccaaugacuagagg
caccuauucucaaacuuuaaauggguaagaggcccggcucgcuggcgcug
gagccgggcguggaaugcgacgcgccuagugggccauuuuugguaagcag
aacuggugcugcgggaugaaccgaacgccggguuaaggcgcccgaugccg
acgcucaucagaccccauaaaagguguugguugauauagacagcccgaau
caacuagcccugaaaauggauggcgcuggagcgucgggcccauacccggc
cgucgacggcagcugcaagccucgacgaguaggagggccgccgcgguggc
gccgaagcccagggcgcgggcccggguggagccgccgcgggcgcagaucu
uggugguaguagcaaauauucaaacgagagcuuugaaggccgaaguggag
aaggguuccaugugaacagcaguugaacaugggugagccgguccuaaggg
acgggccuacgccguucggaggggagggccccgcucgaccgaaagggagu
cggguccagauccccgagcccggagcggcggagacgggcggcccagugcg
gugacgcaaacgaacccggagaugccggcgggugccccgggaaagaguuc
ucuuuucuuugugaagggcagggcgcccuggaacggguucgccccgagag
aggggcccgcgcccuggaaagcgccgcgcugcggcguccggugagcucuc
gucggcccuugaaaauccgggggagaagguguaaaucucgcgccgggccg
uacccauauccgcagcaggucuccaaggugaacagccucuggcguguugg
aacaaggcagaguaagggaagucggcaagucagauccguaacuucgggau
aaggauuggcucuaagggcugagcagccagcuuagaacugucgcggacca
ggggaauccgacuguuuaauuaaaacaaagcaucgcgaaggcccucggcg
gguguugacgcgaugugauuucugcccagugcucugaaugucaaagugaa
gaaauucaacgaagcgcggguaaacggcggucuuaagguagccaaaugcc
ucgucaucuaauuagugacgcgcaugaauggaugaacgagauucccacug
ucccuaccugcuaucuagcgaaaccacagccaagggaacgggcuuggcag
aaucagcggggaaagaagacccuguugagcuugacucuagucuggcccug
ugaagccucacuuacccggugaggcggguucuggcgucaagcgccccgcg
gggcgcgacccgccccggggacagcgucagguggggaguuugacuggggc
gguacaccugucaaacgguaacgcagguguccuaaggcgagcucaggggg
gacagaaaccucccguagagcagaagggcaaaagcucgcuugaucuugau
uuucaguaugaguacggaccgcgaaagcggggccucacgauccuuccggc
uuuugggguuuuaagcgggaggugucagaaaaguuaccacagggauaacu
ggcuuguggcggccaagcguucauagcgacgucgcuuuuugauccuucga
ugucggcucuuccuaucauugugaagcagaauucaccaagcguuggauug
uucacccacuaacagggaacgugagcuggguuuagaccgucgugagacag
guuaguuuuacccuacugaugugagccguuguugcaauaguaaucccgcu
caguacgagaggaaccgcggguucagacauuugguucgugcgcuuggcug
aggagccacuggcgcgaagccaccaucugcgggauuaugacugaacgccu
cuaagucagaaucccgccuaaaagcaacgauagcgccgucggaucuccga
uaggccccggguaaccgggaccccggcgcggagagccauucgugacagga
gcggcuagaacgagcgccgcccccucuuccagugacgcaccgcauguuug
uggggaacccggugcuuaaaugacucguagacgaccugauucugggucgg
ggugucgugcguggcagagcagcgcugcgauccauugaaagucagcccuc
gauccaaguuuug

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7oyb A molecular network of conserved factors keeps ribosomes dormant in the egg.
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): G2 R3 V4 G7 Q8 R9 K10 G11 S14 V15 K17 A18 H19 V20 K21 H22 R23 G25 H31 F34 R37 H38 G39 Y40 I44 H50 P52 R54 R64 Y67 R68 F69 K70 K71 R72 T84 G85 F87 Y89 A94 Q95 E118 K119 G121 R123 K125 L126 A127 R128 A129 S130 G131 N132 K145 L150 P151 S152 K156 G173 R174 I175 K177 I179 L180 K181 A182 G183 R184 Y186 H187 K192 R193 N194 W196 R198 V199 R200 G201 V202 A203 M204 N205 P206 V207 E208 H209 G213 G214 N215 H216 Q217 H218 G220 K221 P222 S223 T224 I225 R226 R227 D228 P230 A231 G232 R233 K234 V235 G236 L237 I238 A239 A240 R241 R242 T243 G244 R245
• Binding residue (residue number reindexed from 1): G1 R2 V3 G6 Q7 R8 K9 G10 S13 V14 K16 A17 H18 V19 K20 H21 R22 G24 H30 F33 R36 H37 G38 Y39 I43 H49 P51 R53 R63 Y66 R67 F68 K69 K70 R71 T83 G84 F86 Y88 A93 Q94 E117 K118 G120 R122 K124 L125 A126 R127 A128 S129 G130 N131 K144 L149 P150 S151 K155 G172 R173 I174 K176 I178 L179 K180 A181 G182 R183 Y185 H186 K191 R192 N193 W195 R197 V198 R199 G200 V201 A202 M203 N204 P205 V206 E207 H208 G212 G213 N214 H215 Q216 H217 G219 K220 P221 S222 T223 I224 R225 R226 D227 P229 A230 G231 R232 K233 V234 G235 L236 I237 A238 A239 R240 R241 T242 G243 R244

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7oyb, PDBe:7oyb, PDBj:7oyb
• PDBsum: 7oyb
• PubMed: 36653451
• UniProt: Q6P0V6|RL8_DANRE Large ribosomal subunit protein uL2 (Gene Name=rpl8)