Structure of PDB 7obr Chain V Binding Site BS01

Receptor Information

>7obr Chain V (length=131) Species: 9986 (Oryctolagus cuniculus)

SGAKFRISLGLPVGAVINCADNTGAKNLYIISVKGIKGRLNRLPAAGVGD
MVMATVKKGKPELRKKVHPAVVIRQRKSYRRKDGVFLYFEDNAGVIVNNK
GEMKGSAITGPVAKECADLWPRIASNAGSIA

Ligand information

>7obr Chain 5 (length=3493)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccgguucaacccggcggcggguccggccgugucggcgggucc
cccgaccggcgaccggccgccgccgggcgcauuuccaccgcggcggugcg
ccgcgaccggcuccgggacggcugggaaggcccggcggggaagguggcuc
ggccgaguguuacagcccccccggcagcagcacucgccgaaucccggggc
cgagggagcgagacccgucgccgcgcucuccccccucgggggggccgggc
caccccucccacggcgcgaccgcucggggcggacuguccccagugcgccc
cgggcgggucgcgccgucgggcccgggggaggggccacgcggcgagcgca
cggggucggcggcgacgucggcuacccacccgacccgucuugaaacacgg
accaaggagucuaacacgugcgcgagucgggggcucgcacgaaagccgcc
guggcgcaaugaaggugaaggccggcgcgcucgccggccgaggugggauc
ccgaggccucuccaguccgccgagggcgcaccaccggcccgucucgcccg
ccgcgccggggagguggagcacgagcgcacguguuaggacccgaaagaug
gugaacuaugccugggcagggcgaagccagaggaaacucugguggagguc
cguagcgguccugacgugcaaaucggucguccgaccuggguauaggggcg
aaagacuaaucgaaccaucuaguagcugguucccuccgaaguuucccuca
ggauagcuggcgcucucgcacacgcaguuuuauccgguaaagcgaaugau
uagaggucuuggggccgaaacgaucucaaccuauucucaaacuuuaaaug
gguaagaagcccggcucgcuggcgugagccgggcguggaauggagugccu
agugggccacuuuugguaagcagaacuggcgcugcgggaugaaccgaacg
ccggguuaaggcgcccgaugccgacgcucaucagaccccagaaaaggugu
ugguugauauagagccgaaucaacuagcccugaaaauggauggcgcugga
gcgucgggcccauacccggccgucgccggcagucgagaguggacgggagc
ccgcccccggagccccgcggacgcuacgccgcgacgaguaggagggccgc
ugcggugagccuugaagccuagggcgcgggcccggguggagccgccgcag
gugcagaucuuggugguaguagcaaauauucaaacgagaacuuugaaggc
cgaaguggagaaggguuccaugugaacagcaguugaacaugggucagucg
guccugagagaugggcgagcgccguuccgaagggacgggcgauggccucc
guugcccucggccgaucgaaagggagucggguucagauccccgaauccgg
aguggcggagaugggcgccgcgaggcguccagugcgguaacgcgaccgau
cccggagaagccggcgggagccccggggagaguucucuuuucuuugugaa
gggcagggcgcccuggaauggguucgccccgagagaggggcccgugccuu
ggaaagcgucgcgguuccggcggcguccggugagcucucgcuggcccuug
aaaauccgggggagaggguguaaaucucgcgccgggccguacccauaucc
gcagcaggucuccaaggugaacagccucuggcauguuggaacaauguagg
uaagggaagucggcaagccggauccguaacuucgggauaaggauuggcuc
uaagggcugggucggucgucggccggcgccuagcagccgacuuagaacug
gugcggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaag
gcccgcggcggguguugacgcgaugugauuucugcccagugcucugaaug
ucaaagugaagaaauucaaugaagcgcggguaaacggcgggaguaacuau
gacucucuuaagguagccaaaugccucgucaucuaauuagugacgcgcau
gaauggaugaacgagauucccacugucccuaccuacuauccagcgaaacc
acagccaagggaacgggcuuggcggaaucagcggggaaagaagacccugu
ugagcuugacucuagucuggcacggugaagagacauguuuuuucacugac
ccggugaggcgggggggcgcucgcuucuggcgccaagcgcccggccgcgc
gccggccgggcgcgacccgcuccggggacagugccagguggggaguuuga
cuggggcgguacaccugucaaacgguaacgcagguguccuaaggcgagcu
cagggaggacagaaaccucccguggagcagaagggcaaaagcucgcuuga
ucuugauuuucaguacgaauacagaccgugaaagcggggccucacgaucc
uucugaccuuuuggguuuuaagcaggaggugucagaaaaguuaccacagg
gauaacuggcuuguggcggccaagcguucauagcgacgucgcuuuuugau
ccuucgaugucggcucuuccuaucauugugaagcagaauucaccaagcgu
uggauuguucacccacuaauagggaacgugagcuggguuuagaccgucgu
gagacagguuaguuuuacccuacugaugauguguuguugccaugguaauc
cugcucaguacgagaggaaccgcagguucagacauuugguguaugugcuu
ggcugaggagccaauggggcgaagcuaccaucugugggauuaugacugaa
cgccucuaagucagaaucccgcccaggcggaacgauacggcagcgccgcg
gagccucgguuggccucggauagccggucccccgcgggguccggugcgga
gugcccuucguccugggaaacggggcgcggccggagaggcggccgccccc
ucgcccgucacgcacgccguucguggggaaccuggcgcuaaaccauucgu
agacgaccugcuucugggucgggguuucguacguagcagagcagcucccu
cgcugcgaucuauugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7obr Molecular mechanism of cargo recognition and handover by the mammalian signal recognition particle.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): A12 R15 S17 G19 P21 A24 V25 I40 S41 K43 G44 I45 K46 G47 R48 L49 N50 R51 L52 T64 K74 V76 R85 K86 R89 F95 N101
• Binding residue (residue number reindexed from 1): A3 R6 S8 G10 P12 A15 V16 I31 S32 K34 G35 I36 K37 G38 R39 L40 N41 R42 L43 T55 K65 V67 R76 K77 R80 F86 N92

Gene Ontology

Molecular Function

• GO:0001223 transcription coactivator binding
• GO:0003735 structural constituent of ribosome
• GO:0031625 ubiquitin protein ligase binding
• GO:0070180 large ribosomal subunit rRNA binding
• GO:1990948 ubiquitin ligase inhibitor activity

Biological Process

• GO:0000122 negative regulation of transcription by RNA polymerase II
• GO:0006412 translation
• GO:0008284 positive regulation of cell population proliferation
• GO:0010628 positive regulation of gene expression
• GO:0032986 protein-DNA complex disassembly
• GO:0050821 protein stabilization
• GO:0070314 G1 to G0 transition
• GO:0072717 cellular response to actinomycin D
• GO:1901798 positive regulation of signal transduction by p53 class mediator
• GO:1903450 regulation of G1 to G0 transition
• GO:1904667 negative regulation of ubiquitin protein ligase activity
• GO:2000059 negative regulation of ubiquitin-dependent protein catabolic process

Cellular Component

• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0032991 protein-containing complex
• GO:0045202 synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7obr, PDBe:7obr, PDBj:7obr
• PDBsum: 7obr
• PubMed: 34260909
• UniProt: G1T6D1|RL23_RABIT Large ribosomal subunit protein uL14 (Gene Name=RPL23)