Structure of PDB 7qgg Chain K Binding Site BS02

Receptor Information

>7qgg Chain K (length=208) Species: 10116 (Rattus norvegicus)

RRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHM
VSDEYEQLSSEALEAARICANKYMVKSCGKDGFHIRVRLHPFHVIRINKM
LSADRLQTGMRGAFGKPQGTVARVHIGQVIMSIRTKLQNKEHVIEALRRA
KFKFPGRQKIHISKKWGFTKFNADEFEDMVAEKRLIPDGCGVKYIPNRGP
LDKWRALH

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): R3 R4 A6 R7 C8 K13 N14 K15 P16 Y17 F22 R24 D35 K39 E63 A67 R90 H92 F94 R98 M102 A108 R110 Q112 M115 R116 A118 F119 Q133 F157 K158 P160 D193 G194 K198 R210
• Binding residue (residue number reindexed from 1): R1 R2 A4 R5 C6 K11 N12 K13 P14 Y15 F20 R22 D33 K37 E61 A65 R88 H90 F92 R96 M100 A103 R105 Q107 M110 R111 A113 F114 Q128 F152 K153 P155 D188 G189 K193 R205

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0045182 translation regulator activity

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0000122 negative regulation of transcription by RNA polymerase II
• GO:0006412 translation
• GO:0006417 regulation of translation
• GO:0043066 negative regulation of apoptotic process
• GO:0097421 liver regeneration
• GO:1990403 embryonic brain development

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005790 smooth endoplasmic reticulum
• 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:7qgg, PDBe:7qgg, PDBj:7qgg
• PDBsum: 7qgg
• PubMed: 36038000
• UniProt: Q6PDV7|RL10_RAT Large ribosomal subunit protein uL16 (Gene Name=Rpl10)