Structure of PDB 7cpv Chain LL Binding Site BS01

Receptor Information

>7cpv Chain LL (length=206) Species: 10090 (Mus musculus)

APSRNGMILKPHFHKDWQQRVDTWFNQPARKIRRRKARQAKARRIAPRPA
SGPIRPIVRCPTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPR
RRNKSTESLQANVQRLKEYRSKLILFPRKPSAPKKGDSSAEELKLATQLT
GPVMPIRNVYKKEKARVITEEEKNFKAFASLRMARANARLFGIRAKRAKE
AAEQDV

Ligand information

>7cpv Chain L5 (length=3541)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggaaaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccgcgcgucgcggcgugggaaau
guggcguacggaagacccacuccccgggggggcccaaguccuucugaucg
aggcccagcccguggacggugugaggccgguagcggccccggcgcgccgg
gcucgggucuucccggagucggguugcuugggaaugcagcccaaagcggg
ugguaaacuccaucuaaggcuaaauaccggcacgagaccgauagucaaca
aguaccguaagggaaaguugaaaagaacuuugaagagagaguucaagagg
gcgugaaaccguuaagagguaaacgggugggguccgcgcaguccgcccgg
aggauucaacccggcggcggccggccgugcccggggcggaucugcggggg
accgucccccggccggcgaccggccgccgccgggcgcacuuccaccgugg
cggugcgccgcgaccggcuccgggacggccgggaaggcccgguggggaag
guggcucgggcccgaguguuacagcccuccggccgcgcuuucgccgaauc
ccggggccgaggaagcgucgccgcgcucucccucgggggccgggccgccc
cucccacggcgcgaccgcucggggcggacuguccccagugcgccccgggc
guggucgcgccgucggguccgggggcggucacgcgugagcgcacgggguc
ggcggcgaugucggcuacccacccgacccgucuugaaacacggaccaagg
agucuaacgcgugcgcgagucaggggcucguccgaaagccgccguggcgc
aaugaaggugaagggccccgcccgggggcccgaggugggaucccgaggcc
ucuccaguccgccgagggcgcaccaccggcccgucucgcccgccgcgccg
gggagguggagcacgagcguacgcguuaggacccgaaagauggugaacua
ugcuugggcagggcgaagccagaggaaacucugguggagguccguagcgg
uccugacgugcaaaucggucguccgaccuggguauaggggcgaaagacua
aucgaaccaucuaguagcugguucccuccgaaguuucccucaggauagcu
ggcgcucucgccgcaguuuuauccgguaaagcgaaugauuagaggucuug
gggccgaaacgaucucaaccuauucucaaacuuuaaauggguaagaagcc
cggcucgcuggcguggagccgggcguggaaugcgagugccuagugggcca
cuuuugguaagcagaacuggcgcugcgggaugaaccgaacgccggguuaa
ggcgcccgaugccgacgcucaucagaccccagaaaagguguugguugaua
uagacagcaggacgguggccauggaagucggaauccgcuaaggagugugu
aacaacucaccugccgaaucaacuagcccugaaaauggauggcgcuggag
cgucgggcccauacccggccgucgccggcaguggaacgggacgggagccc
cgcggacgcuacgccgcgacgaguaggagggccgcugcggugagccuuga
agccuagggcgcgggcccggguggagccgccgcaggugcagaucuuggug
guaguagcaaauauucaaacgagaacuuugaaggccgaaguggagaaggg
uuccaugugaacagcaguugaacaugggucagucgguccugagagauggg
cgagugccguuccgaagggacgggcgauggccuccguugcccucggccga
ucgaaagggagucggguucagauccccgaauccggaguggcggagauggg
cgccgcgaggccagugcgguaacgcgaccgaucccggagaagccggcggg
agccccggggagaguucucuuuucuuugugaagggcagggcgcccuggaa
uggguucgccccgagagaggggcccgugccuuggaaagcgucgcgguucc
ggcggcguccggugagcucucgcuggcccuugaaaauccgggggagaggg
uguaaaucucgcgccgggccguacccauauccgcagcaggucuccaaggu
gaacagccucuggcauguuggaacaauguagguaagggaagucggcaagc
cggauccguaacuucgggauaaggauuggcucuaagggcugggucggggc
cggcgccuagcagccgacuuagaacuggugcggaccaggggaauccgacu
guuuaauuaaaacaaagcaucgcgaaggcccgcggcggguguugacgcga
ugugauuucugcccagugcucugaaugucaaagugaagaaauucaaugaa
gcgcggguaaacggcgggaguaacuaugacucucuuaagguagccaaaug
ccucgucaucuaauuagugacgcgcaugaauggaugaacgagauucccac
ugucccuaccuacuauccagcgaaaccacagccaagggaacgggcuuggc
ggaaucagcggggaaagaagacccuguugagcuugacucuagucuggcac
ggugaagagacaugcucaucguuuuuucacugacccggugaggcgggggg
gcgagccccgaggggcucucgcuucuggcgccaagcguccgucccgggcg
ggcgcgacccgcuccggggacagugccagguggggaguuugacuggggcg
guacaccugucaaacgguaacgcagguguccuaaggcgagcucagggagg
acagaaaccucccguggagcagaagggcaaaagcucgcuugaucuugauu
uucaguacgaauacagaccgugaaagcggggccucacgauccuucugacc
uuuuggguuuuaagcaggaggugucagaaaaguuaccacagggauaacug
gcuuguggcggccaagcguucauagcgacgucgcuuuuugauccuucgau
gucggcucuuccuaucauugugaagcagaauucaccaagcguuggauugu
ucacccacuaauagggaacgugagcuggguuuagaccgucgugagacagg
uuaguuuuacccuacugaugauguguuguugccaugguaauccugcucag
uacgagaggaaccgcagguucagacauuugguguaugugcuuggcugagg
agccaauggggcgaagcuaccaucugugggauuaugacugaacgccucua
agucagaaucccgcccaggcggaacgauacggcagcgccgaaggagccuc
gguuggccccggauagccggguccccgccgggguccggugcggagagccg
uucgucuugggaaacggggugcggccggaaaggcggccgcccucucgccc
gucacguugaacgcacguucguguggaaccuggcgcuaaaccauucguag
acgaccugcuucugggucgggguuucguacguagcagagcagcucccucg
cugcgaucuauugaaagucagcccucgacacaaggguuugu

.........................<<<<<<.....<......>......
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>>>>>>..<<<..<<<<<...<<<<<<<<<<.....>>>>>>.>>>>...
..>>>>>..<<<<<<<<<....<<<<..<<<<<<<....<<<<......>
>>>.....((......<<<.....))>>>...>.>>>>>>.......>>>
>...>>>>>>>>>.......<<<<<<<........>>>>>>>.....<<<
<<..((((((>>>>>..>>>..............................
....<<....>>...............<<<......>>>...........
.......................<<<<<<<<..<<<.<<...<<<<<<<<
.<<<.....<<<<<<<<<<<<<<<<<<..<..<<<<<<<.<<<.....>>
>>>>>>>>..>..>>>>...>>>>>>>>>>>>>>......>>>.>>>.>>
>>>...<<<<<<<<<<<<<<<<<<<<<<<...<<.<<<<.<<.<<<<...
...<<<<<<..>>>>>>.......>>>>>>>>>>......>>>>>>..>>
>>>>>>>>>.............<<<<<<.<<<<..>>>>.<<<<<<<<<<
<.<<<<<<<<<<..<<<<<.<<<<<.<...........>..>>>>>.>>>
>.>...>>>>>>>.>>>...>>>>.>>>>>.>>...>>>>>>.....>>>
.>>>>>...>>>>>...>>>>>>>>..<<<<........>>>><<<<<<.
...<<<<<<<<<<<<<..<<<...<<<<........>>>>.....>>>..
.<<....>>...<<<<<<<.....>>>>>>>..<<<<<...<<<..<<<.
..[[...{[[>>>..>>>....>>>>>.<<<<<<<<<.<<<<......>>
>>>>>>>>>.>>....>>>>>>>>>>>>>..<<.<..<<<<<<<.....<
<<<<<<<<..<<<....<<<<<<<....>>>>>>>.....>>>...<<<.
.<<.<<........>>>>.>>>....>>>>>>>>>...<<.......>>.
.....>>>>>>...>..>.>>..<<<<<<....<.<<<....>>>.><<.
<<<<<<<.....<<<.<<<<<<<<<...<<<....<<<..<.<<<....<
<.............>>..>>>.>..>>>..>.>>...>>>>>>>...<<<
<<<<<<.........>>>>>>>>>....>>>>>>>>>>>>..>>..<<<<
.<<<<<.....>>>>>.>>>>....<<<......>>>...<<<<<<<...
<<<(((.......<<<<<.....<<..........<<<.<<<<<<<<<<.
......<..<........................................
...........>.>...>>>>>>>>>>>>>..........))).>>...>
>>>>..>>>...>>>>>>><<<<<<.<<<...]].}..]]..........
............>>>>>>>>>....>>>>>>...<<<<<<<<.<<.....
.<<<<.<<<<....>>>>>>>>...>>>>>>>>>>........>>>>>><
<.....<<.....<<<<<<.......>>>>>>.<<<.....<<<<<.<<.
..<<<<<<...<<.....>>.>>>>>>....((<<<<<<...<<....<<
<....>>>..........<<.<<<<<...........>>>>>>>......
>>....>>>..<<<<<........>>>>>))<<<<....<<<<<..<<<.
<.<...>..>>>>..<<<....>>>...<..<<<<<<<...<<<<<<<<<
<<<.<<<<<<<<<<..[[[..>>>>>>....<<<<<.<<<<.<<<<....
.<<<.....>>>.....>>>>>>>>..>>>>>.....<<<<<<<......
.>>>>>>>>>>>...>>>>>>>>>>>>.........>>>>>>>..>....
......>>.>>>.>>>>.>>>..>>.....<<......>>>>>>>.<<<<
.....>>>>..>>>....<<<<.....<<<<<<<.<<.............
..<<<<<....<<..>>.....>>>>><<.<<<<<<<<<<<.........
..........>>>>>..>>>>>>.>>............<<<<<<<<<..<
<<.........>>>..<<<<<<<....<<<<.....>>>>......>>>>
>>>...<<..<<<..<<<<<<....<<<.....<<<<....>>>>.....
>>>.>>>>..>>>>><<<<<<.......>>>>>>........<.......
....<<<<<.......>>>>>.....>.....>>....>>.>>>>>>>..
...>>.>>>>>>>..>>>>>>....>>....<<<<<........>>>>>.
...<<<<<..<<<.<<......<<<<.<<<<<<..<<<<<.<<<<<<<<<
.<<<<<<<<<<<<....>>.>>>>>>>>>>...<<<<<.....<<<<...
..................................<<<<<<<<<..>>.>>
>>>>>..>>>>..>>>>>....>>>>>>>>>..>>>>>...<<<.....>
>>..<<<<<<...........>>>>>>..<<...<<<<<<<...<<<<<<
.......>>>>>>.....<<.[.(((>>....>>>>>>>...<<<..<<<
<.......>>>>..>>><<<<....>>>>>>)))].....<<<<<<<..<
<<..)))))).>>>>>>>>>>.........>>>>..>>>>>>.......<
<.<...<<<<<<...<<.......>>...>>>>>>....>.>.>......
.<<<<<.<<<<<<..<.<.<<<<<......>>>>>...>.>.<<<.....
....>>>.....>>>>>..>...>>>.>>....<<<<<<<....>>>.>>
>>....>>..>>>.>>>>>.....<<<<<<.<..<<<....<<<<<....
.............>>>>>..<<<<....<<<<...<<<.<<<<<<<]]].
>>>>>..>>.>>>..>>>>...>>>><<<<<...<<<<<...........
>>>>>...>>>>>.>>>...>.>>>>>>.....<<<<<<...<<..<<.<
....<<<........<<<<<<<<<<....>>>>>>>>>>.......>>>.
..<<<..<<<<....<<<<...<<<<<......>>>>>..>>>>...>>>
>..>>>................>.>>..>>.>>>>>><<<<<.<......
.......>....<<.<<<<<<<.<<.....<<<<....<<<<<......>
>>>>...>>>>....>>....>>>>.>>>.>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7cpv A male germ-cell-specific ribosome controls male fertility.
• Resolution: 3.03 Å
• Binding residue (original residue number in PDB): A2 S4 R5 M8 L10 K11 H13 F14 H15 K16 W18 Q19 W25 Q28 P29 R31 K32 I33 R35 R36 R39 Q40 R56 V59 R60 C61 P62 T63 Y66 H67 R71 R74 L78 K88 R92 D99 P100 R101 R102 R103 S106 R129 R158 K177 F179 R183 M184 R186 A187 N188 R190 G193 R195 K197 R198
• Binding residue (residue number reindexed from 1): A1 S3 R4 M7 L9 K10 H12 F13 H14 K15 W17 Q18 W24 Q27 P28 R30 K31 I32 R34 R35 R38 Q39 R55 V58 R59 C60 P61 T62 Y65 H66 R70 R73 L77 K87 R91 D98 P99 R100 R101 R102 S105 R128 R157 K176 F178 R182 M183 R185 A186 N187 R189 G192 R194 K196 R197

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0001824 blastocyst development
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0060348 bone development
• GO:0140236 translation at presynapse
• GO:0140242 translation at postsynapse

Cellular Component

• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:0098793 presynapse
• GO:0098794 postsynapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7cpv, PDBe:7cpv, PDBj:7cpv
• PDBsum: 7cpv
• PubMed: 36517592
• UniProt: P47963|RL13_MOUSE Large ribosomal subunit protein eL13 (Gene Name=Rpl13)