Structure of PDB 7oyc Chain f1 Binding Site BS01

Receptor Information

>7oyc Chain f1 (length=107) Species: 8355 (Xenopus laevis)

RLWCKATFAGYKRGLRNQREHTALLKIEGVYARDETEFYFGKRCAYVYKA
KNNTVTPGGKPNRTRVIWGKVTRAHGNSGMVRAKFRSNLPAKAIGHRIRV
MLYPSRI

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): R4 L5 W6 K8 K15 R16 G17 L18 R19 N20 Q21 E23 H24 K29 Y34 R36 R46 Y51 K52 K54 N55 N56 T57 V58 P60 P64 T67 R68 V69 W71 K73 T75 R76 H78 G79 N80 S81 R85 K87 R89 S90 N91 P93 A94 H99 R100 R102 R109
• Binding residue (residue number reindexed from 1): R1 L2 W3 K5 K12 R13 G14 L15 R16 N17 Q18 E20 H21 K26 Y31 R33 R43 Y48 K49 K51 N52 N53 T54 V55 P57 P61 T64 R65 V66 W68 K70 T72 R73 H75 G76 N77 S78 R82 K84 R86 S87 N88 P90 A91 H96 R97 R99 R106

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

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

External links

• PDB: RCSB:7oyc, PDBe:7oyc, PDBj:7oyc
• PDBsum: 7oyc
• PubMed: 36653451
• UniProt: P02434|RL35A_XENLA Large ribosomal subunit protein eL33 (Gene Name=rpl35a)