Structure of PDB 6swa Chain I Binding Site BS01

Receptor Information

>6swa Chain I (length=208) Species: 10090 (Mus musculus)

RRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHM
VSDEYEQLSSEALEAARICANKYMVKSCGKDGFHIRVRLHPFHVIRINKM
LSADRLQTGMRGAFGKPQGTVARVHIGQVIMSIRTKLQNKEHVIEALRRA
KFKFPGRQKIHISKKWGFTKFNADEFEDMVAEKRLIPDGCGVKYIPNRGP
LDKWRALH

Ligand information

>6swa Chain q (length=3612)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggaaaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccgcgcggggcgugggaaaugug
gcguacggaagacccacuccccggcgccgcucguggggggcccaaguccu
ucugaucgaggcccagcccguggacggugugaggccgguagcggccccgg
cgccgggcucgggucuucccggagucggguugcuugggaaugcagcccaa
agcgggugguaaacuccaucuaaggcuaaauaccggcacgagaccgauag
ucaacaaguaccguaagggaaaguugaaaagaacuuugaagagagaguuc
aagagggcgugaaaccguuaagagguaaacgggugggguccgcgcagucc
gcccggaggauucaacccggcggcggguccggccgugucggcggcccggc
ggaucuuucccgcccccggggucggcgggggaccgucccccggaccggcg
accggccgccgccgggcgcauuuccaggcggugcgccgcgaccggcuccg
ggacggcugggaaggcccggcggggaagguggcucggggcccccgagugu
uacagcccccccggcagcagcacucgccgaaucccggggccgagggagcg
agacccgucgccgcgcucuccccccugggggggccgggccaccccuccca
cggcgcgaccgcucucccagggggcggggcggacuguccccagugcgccc
cgggcgggucgcgccgucgggcccggggggccacgcgcgcgucccgggac
ggcggagcgagcgcacggggucggcggcgacgucggcuacccacccgacc
cgucuugaaacacggaccaaggagucuaacacgugcgcgagucgggggcu
cgcacgaaagccgccguggcgcaaugaaggugaaggccggcgcgcucgcc
ggccgaggugggaucccgaggccucuccaguccgccgaggggcaccaccg
gcccgucucgcccgccgcgccggggagguggagcacgagcgcacguguua
ggacccgaaagauggugaacuaugccugggcagggcgaagccagaggaaa
cucugguggagguccguagcgguccugacgugcaaaucggucguccgacc
uggguauaggggcgaaagacuaaucgaaccaucuaguagcugguucccuc
cgaaguuucccucaggauagcuggcgcucucgcccacgcaguuuuauccg
guaaagcgaaugauuagaggucuuggggccgaaacgaucucaaccuauuc
ucaaacuuuaaauggguaagaagcccggcucgcuggcguggagccggggu
ggaaugcgagugccuagugggccacuuuugguaagcagaacuggcgcugc
gggaugaaccgaacgccggguuaaggcgcccgaugccgacgcucaucaga
ccccagaaaagguguugguugauauagacagcaggacgguggccauggaa
gucggaauccgcuaaggaguguguaacaacucaccugccgaaucaacuag
cccugaaaauggauggcgcuggagcgucgggcccauacccggccgucgcc
ggccuacgccgcgacgaguaggagggccgcugcggugagccuugaagccu
agggcgcgggcccggguggagccgccgcaggugcagaucuuggugguagu
agcaaauauucaaacgagaacuuugaaggccgaaguggagaaggguucca
ugugaacagcaguugaacaugggucagucgguccugagagaugggcgagc
gccguuccgaagggacgggcgauggccuccguugcccucggccgaucgaa
agggagucggguucagauccccgaauccggaguggcggagaugggcgccg
cgaggcguccagugcgguaacgcgaccgaucccggagaagccggcgggag
ccccggggagaguucucuuuucuuugugaagggcagggcgcccuggaaug
gguucgccccgagagaggggcccgugccuuggaaagcgucgcaccuuugc
ugggguccggugagcucucgcuggcccuugaaaauccgggggagagggug
uaaaucucgcgccgggccguacccauauccgcagcaggucuccaagguga
acagccucuggcauguuggaacaauguagguaagggaagucggcaagccg
gauccguaacuucgggauaaggauuggcucuaagggcuggcagccgacuu
agaacuggugcggaccaggggaauccgacuguuuaauuaaaacaaagcau
cgcgaaggcccgcggcggguguugacgcgaugugauuucugcccagugcu
cugaaugucaaagugaagaaauucaaugaagcgcggguaaacggcgggag
uaacuaugacucucuuaagguagccaaaugccucgucaucuaauuaguga
cgcgcaugaauggaugaacgagauucccacugucccuaccuacuauccag
cgaaaccacagccaagggaacgggcuuggcggaaucagcggggaaagaag
acccuguugagcuugacucuagucuggcacggugaagagacaugagaggu
guagaauaagugggaggcccgggccgccggugaaauaccacuacucugau
cguuuuuucacugacccggugaggcgggggggcgagcccgaggggcucuc
gcuucuggcgccaagcgcccgcccggccgggcgcgacccgcuccggggac
agugccagguggggaguuugacuggggcgguacaccugucaaacgguaac
gcagguguccuaaggcgagcucagggaggacagaaaccucccguggagca
gaagggcaaaagcucgcuugaucuugauuuucaguacgaauacagaccgu
gaaagcggggccucacgauccuucugaccuuuuggguuuuaagcaggagg
ugucagaaaaguuaccacagggauaacuggcuuguggcggccaagcguuc
auagcgacgucgcuuuuugauccuucgaugucggcucuuccuaucauugu
gaagcagaauucgccaagcguuggauuguucacccacuaauagggaacgu
gagcuggguuuagaccgucgugagacagguuaguuuuacccuacugauga
uguguuguugccaugguaauccugcucaguacgagaggaaccgcagguuc
agacauuugguguaugugcuuggcugaggagccaauggggcgaagcuacc
aucugugggauuaugacugaacgccucuaagucagaaucccgcccaggcg
gaacgauacggcagcgccgcggagccucgguuggccucggauagccgguc
cgggguccggugcggagugcccuucguccugggaaacggggcgcggccgg
aaaggcggccgcccccucgcccgucacgcaccgcacguucguggggaacc
uggcgcuaaaccauucguagacgaccugcuucugggucgggguuucguac
guagcagagcagcucccucgcugcgaucuauugaaagucagcccucgaca
caaggguuuguc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6swa Protein Synthesis in the Developing Neocortex at Near-Atomic Resolution Reveals Ebp1-Mediated Neuronal Proteostasis at the 60S Tunnel Exit.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): R4 P5 A6 R7 C8 K13 N14 K15 P16 Y17 R21 F22 F34 D35 K39 E63 A67 K74 R90 H92 R98 L103 R110 G114 M115 R116 A118 F119 Q133 F157 K158 D193 G194 R210
• Binding residue (residue number reindexed from 1): R2 P3 A4 R5 C6 K11 N12 K13 P14 Y15 R19 F20 F32 D33 K37 E61 A65 K72 R88 H90 R96 L101 R105 G109 M110 R111 A113 F114 Q128 F152 K153 D188 G189 R205

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation
• GO:0006417 regulation of translation
• GO:0140236 translation at presynapse
• GO:0140242 translation at postsynapse
• GO:1990403 embryonic brain development

Cellular Component

• GO:0005737 cytoplasm
• GO:0005790 smooth endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0045202 synapse
• GO:0098793 presynapse
• GO:0098794 postsynapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6swa, PDBe:6swa, PDBj:6swa
• PDBsum: 6swa
• PubMed: 33357414
• UniProt: Q6ZWV3|RL10_MOUSE Large ribosomal subunit protein uL16 (Gene Name=Rpl10)