Structure of PDB 7oyb Chain R1 Binding Site BS02

Receptor Information

>7oyb Chain R1 (length=166) Species: 7955 (Danio rerio)

SMLRLQKRLASSVLRCGKKKVWLDPNETNEIANANSRQQIRKLVKDGLII
KKPVTVHSRARCRKNTLARRKGRHMGVGKRKGTANARMPEKLCWMRRMRI
LRRLLRRYREAKKIDRHMYHSLYLRAKGNVFKNKRILMEHIHKLKADKAR
KKLLADQAEARRTKTR

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): S2 M3 L4 R5 K8 R9 L10 R16 G18 K19 K20 K21 W23 L24 P26 S37 R38 R42 K46 K53 V55 T56 V57 H58 S59 R60 R62 C63 R70 R71 R74 H75 G77 V78 G79 K80 R81 K82 G83 T84 N86 A87 R88 M89 P90 K92 L93 W95 M96 R97 R100 I101 R103 R104 R110 R117 H118 Y120 H121 Y124 L125 K128 N130 N134 K135 R136
• Binding residue (residue number reindexed from 1): S1 M2 L3 R4 K7 R8 L9 R15 G17 K18 K19 K20 W22 L23 P25 S36 R37 R41 K45 K52 V54 T55 V56 H57 S58 R59 R61 C62 R69 R70 R73 H74 G76 V77 G78 K79 R80 K81 G82 T83 N85 A86 R87 M88 P89 K91 L92 W94 M95 R96 R99 I100 R102 R103 R109 R116 H117 Y119 H120 Y123 L124 K127 N129 N133 K134 R135

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation
• GO:0030097 hemopoiesis

Cellular Component

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

External links

• PDB: RCSB:7oyb, PDBe:7oyb, PDBj:7oyb
• PDBsum: 7oyb
• PubMed: 36653451
• UniProt: Q6P5L3|RL19_DANRE Large ribosomal subunit protein eL19 (Gene Name=rpl19)