Structure of PDB 7qgg Chain F Binding Site BS02

Receptor Information

>7qgg Chain F (length=294) Species: 10116 (Rattus norvegicus)

VKVVKNKAYFKRYQVRFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIV
RVTNRDIICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGL
LLARRLLNRFGMDKIYEGQVEVNGDEYNVESIDGQPGAFTCYLDAGLART
TTGNKVFGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIMGQN
VADYMRYLMEEDEDAYKKQFSQYIKNNVTPDMMEEMYKKAHAAIRENPVY
EKKPKREVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAAES

Ligand information

>7qgg Chain t (length=3679)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggaaaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccgcgcgcggcgcgggaaaugug
gcguacggaagacccacuccccggcgccgcucguggggggcccaaguccu
ucugaucgaggcccagcccguggacggugugaggccgguagcggcccccg
gcgcgcgcccgggucuucccggagucggguugcuugggaaugcagcccaa
agcgggugguaaacuccaucuaaggcuaaauaccggcacgagaccgauag
ccaacaaguaccguaagggaaaguugaaaagaacuuugaagagagaguuc
aagagggcgugaaaccguuaagagguaaacgggugggguccgcgcagucc
gcccggaggauucaacccggcggcgcgcguccggccgugccgguggccgg
cggaucuuucccgcucccggugucggcgggggaccgccccccggaucggc
gaccggccgccgccgggcgcacuuccaggcggugcgccgcgaccggcucc
gggacggcugggaaggcccggcggggaagguggcucggggccccgagugu
uacagccccccggcagcagcgcucgccgaaucccggggccgagggagccg
gauacccgucgccgcgcucuccccccggcgggggccgggccgccccuccc
acggcgcgaccgcucucccagggggcggggcggacuguccccagugcgcc
ccgggcgucgucgcgccgucgggcccgggcgcgcucucccuccccuucuc
ggggugggggggagcgagagcgcacggggucggcggcgaugucggcuacc
cacccgacccgucuugaaacacggaccaaggagucuaacgcgugcgcgag
ucaggggcucguccgaaagccgccguggcgcaaugaaggugaagggcccc
guucccgggggccgaggugggaucccgaggccucuccaguccgccgaggg
gcaccaccggcccgucucgcccgccgcgccggggagguggagcacgagcg
uacgcguuaggacccgaaagauggugaacuaugccugggcagggcgaagc
cagaggaaacucugguggagguccguagcgguccugacgugcaaaucggu
cguccgaccuggguauaggggcgaaagacuaaucgaaccaucuaguagcu
gguucccuccgaaguuucccucaggauagcuggcgcucucgcaacgcggu
cgacaacccgcaguuuuauccgguaaagcgaaugauuagaggucuugggg
ccgaaacgaucucaaccuauucucaaacuuuaaauggguaagaagcccgg
cucgcuggcguggagccgggcguggaaugcgagugccuagugggccacuu
uugguaagcagaacuggcgcugcgggaugaaccgaacgccggguuaaggc
gcccgaugccgacgcucaucagaccccagaaaagguguugguugauauag
acagcaggacgguggccauggaagucggaauccgcuaggaguguguaaca
acucaccugccgaaucaacuagcccugaaaauggauggcgcuggagcguc
gggcccauacccggccgucgccggcgucggaacgggacgggagcggccgc
ucgggccccgcggacgcuacgccgcgacgaguaggagggccgcugcggug
agccuugaagccuagggcgcgggcccggguggagccgccgcaggugcaga
ucuuggugguaguagcaaauauucaaacgagaacuuugaaggccgaagug
gagaaggguuccaugugaacagcaguugaacaugggucagucgguccuga
gagaugggcgagugccguuccgaagggacgggcgauggccuccguugccc
ucagccgaucgaaagggagucggguucagauccccgaauccggaguggcg
gagaugggcgccgcgaggcguccagugcgguaacgcgaccgaucccggag
aagccggcgggagccccggggagaguucucuuuucuuugugaagggcagg
gcgcccuggaauggguucgccccgagagaggggcccgugccuuggaaagc
gucgcaguuccggcggcguccggugagcucucgcuggcccuugaaaaucc
gggggagaggguguaaaucucgcgccgggccguacccauauccgcagcag
gucuccaaggugaacagccucuggcauguuggaacaauguagguaaggga
agucggcaagccggauccguaacuucgggauaaggauuggcucuaagggc
uggcagccgacuuagaacuggugcggaccaggggaauccgacuguuuaau
uaaaacaaagcaucgcgaaggcccgcggcggguguugacgcgaugugauu
ucugcccagugcucugaaugucaaagugaagaaauucaaugaagcgcggg
uaaacggcgggaguaacuaugacucucuuaagguagccaaaugccucguc
aucuaauuagugacgcgcaugaauggaugaacgagauucccacugucccu
accuacuauccagcgaaaccacagccaagggaacgggcuuggcggaauca
gcggggaaagaagacccuguugagcuugacucuagucuggcacggugaag
agacaugagagguguagaauaagugggaggcccgggccgccggugaaaua
ccacuacucucaucguuuuuucacugacccggugaggcgggggggcgagc
cccgaggggcucucgcuucuggcgccaagcgcccgucgggcgggcgcgac
ccgcuccggggacagugccagguggggaguuugacuggggcgguacaccu
gucaaacgguaacgcagguguccuaaggcgagcucagggaggacagaaac
cucccguggagcagaagggcaaaagcucgcuugaucuugauuuucaguac
gaauacagaccgugaaagcggggccucacgauccuucugaccuuuugggu
uuuaagcaggaggugucagaaaaguuaccacagggauaacuggcuugugg
cggccaagcguucauagcgacgucgcuuuuugauccuucgaugucggcuc
uuccuaucauugugaagcagaauucaccaagcguuggauuguucacccac
uaauagggaacgugagcuggguuuagaccgucgugagacagguuaguuuu
acccuacugaugauguguuguugccaugguaauccugcucaguacgagag
gaaccgcagguucagacauuugguguaugugcuuggcugaggagccaaug
gggcgaagcuaccaucugugggauuaugacugaacgccucuaagucagaa
ucccgcccaggcggaacgauacggcagcgccgaaggagccucgguuggcc
ccggauagccggcucccgggguccggugcggagagccauucgucccggga
aacggggugcggccggaaagggggccgcccucucgcccgucacgcuuaac
gcacguucguguggaaccuggcgcuaaaccauucguagacgaccugcuuc
ugggucgggguuucguacguagcagagcagcucccucgcugcgaucuauu
gaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7qgg Neuronal RNA granules are ribosome complexes stalled at the pre-translocation state.
• Resolution: 2.86 Å
• Binding residue (original residue number in PDB): V4 K5 K10 A11 R15 Y16 Q17 R23 G26 T28 D29 R35 L36 K43 Y44 K48 F113 P139 G140 Y145 L150 R152 T153 F160 S176 R179 R268 S272 A274 Q275 D278 R279 Q282 K283 S286 F287 R289 A290
• Binding residue (residue number reindexed from 1): V1 K2 K7 A8 R12 Y13 Q14 R20 G23 T25 D26 R32 L33 K40 Y41 K45 F110 P136 G137 Y142 L147 R149 T150 F157 S173 R176 R265 S269 A271 Q272 D275 R276 Q279 K280 S283 F284 R286 A287

Gene Ontology

Molecular Function

• GO:0003729 mRNA binding
• GO:0003730 mRNA 3'-UTR binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding
• GO:0031625 ubiquitin protein ligase binding
• GO:0048027 mRNA 5'-UTR binding
• GO:1990948 ubiquitin ligase inhibitor activity

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0010628 positive regulation of gene expression
• GO:0042273 ribosomal large subunit biogenesis
• GO:0045727 positive regulation of translation
• GO:0050821 protein stabilization
• GO:1901796 regulation of signal transduction by p53 class mediator
• GO:2000059 negative regulation of ubiquitin-dependent protein catabolic process
• GO:2000435 negative regulation of protein neddylation

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0014069 postsynaptic density
• GO:0017101 aminoacyl-tRNA synthetase multienzyme complex
• 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:7qgg, PDBe:7qgg, PDBj:7qgg
• PDBsum: 7qgg
• PubMed: 36038000
• UniProt: P09895|RL5_RAT Large ribosomal subunit protein uL18 (Gene Name=Rpl5)