Structure of PDB 7cpu Chain LR Binding Site BS01

Receptor Information

>7cpu Chain LR (length=174) Species: 10090 (Mus musculus)

SMLRLQKRLASSVLRCGKKKVWLDPNETNEIANANSRQQIRKLIKDGLII
RKPVTVHSRARCRKNTLARRKGRHMGIGKRKGTANARMPEKVTWMRRMRI
LRRLLRRYRESKKIDRHMYHSLYLKVKGNVFKNKRILMEHIHKLKADKAR
KKLLADQAEARRSKTKEARKRREE

Ligand information

>7cpu Chain L5 (length=3539)

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
cggauccguaacuucgggauaaggauuggcucuaagggcugggucggccg
gcgccuagcagccgacuuagaacuggugcggaccaggggaauccgacugu
uuaauuaaaacaaagcaucgcgaaggcccgcggcggguguugacgcgaug
ugauuucugcccagugcucugaaugucaaagugaagaaauucaaugaagc
gcggguaaacggcgggaguaacuaugacucucuuaagguagccaaaugcc
ucgucaucuaauuagugacgcgcaugaauggaugaacgagauucccacug
ucccuaccuacuauccagcgaaaccacagccaagggaacgggcuuggcgg
aaucagcggggaaagaagacccuguugagcuugacucuagucuggcacgg
ugaagagacaugcucaucguuuuuucacugacccggugaggcgggggggc
gagccccgaggggcucucgcuucuggcgccaagcguccgucccgggcggg
cgcgacccgcuccggggacagugccagguggggaguuugacuggggcggu
acaccugucaaacgguaacgcagguguccuaaggcgagcucagggaggac
agaaaccucccguggagcagaagggcaaaagcucgcuugaucuugauuuu
caguacgaauacagaccgugaaagcggggccucacgauccuucugaccuu
uuggguuuuaagcaggaggugucagaaaaguuaccacagggauaacuggc
uuguggcggccaagcguucauagcgacgucgcuuuuugauccuucgaugu
cggcucuuccuaucauugugaagcagaauucaccaagcguuggauuguuc
acccacuaauagggaacgugagcuggguuuagaccgucgugagacagguu
aguuuuacccuacugaugauguguuguugccaugguaauccugcucagua
cgagaggaaccgcagguucagacauuugguguaugugcuuggcugaggag
ccaauggggcgaagcuaccaucugugggauuaugacugaacgccucuaag
ucagaaucccgcccaggcggaacgauacggcagcgccgaaggagccucgg
uuggccccggauagccggguccccgccgggguccggugcggagagccguu
cgucuugggaaacggggugcggccggaaaggcggccgcccucucgcccgu
cacguugaacgcacguucguguggaaccuggcgcuaaaccauucguagac
gaccugcuucugggucgggguuucguacguagcagagcagcucccucgcu
gcgaucuauugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7cpu A male germ-cell-specific ribosome controls male fertility.
• Resolution: 2.82 Å
• Binding residue (original residue number in PDB): M3 L4 R5 K8 R9 L10 R16 G18 K19 K20 K21 W23 L24 P26 S37 R38 Q39 R42 K43 K46 V55 T56 H58 S59 R60 A61 R62 C63 R64 R71 R74 H75 M76 G77 I78 G79 R81 K82 G83 T84 N86 A87 R88 P90 K92 W95 M96 R100 I101 R103 R104 R108 R110 R117 H118 Y120 H121 Y124 L125 K128 G129 N130 N134 K135 R136 H143
• Binding residue (residue number reindexed from 1): M2 L3 R4 K7 R8 L9 R15 G17 K18 K19 K20 W22 L23 P25 S36 R37 Q38 R41 K42 K45 V54 T55 H57 S58 R59 A60 R61 C62 R63 R70 R73 H74 M75 G76 I77 G78 R80 K81 G82 T83 N85 A86 R87 P89 K91 W94 M95 R99 I100 R102 R103 R107 R109 R116 H117 Y119 H120 Y123 L124 K127 G128 N129 N133 K134 R135 H142

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7cpu, PDBe:7cpu, PDBj:7cpu
• PDBsum: 7cpu
• PubMed: 36517592
• UniProt: P84099|RL19_MOUSE Large ribosomal subunit protein eL19 (Gene Name=Rpl19)