Structure of PDB 6swa Chain M Binding Site BS01

Receptor Information

>6swa Chain M (length=203) Species: 10090 (Mus musculus)

GAYKYIQELWRKKQSDVMRFLLRVRCWQYRQLSALHRAPRPTRPDKARRL
GYKAKQGYVIYRIRVRRGGRKRPVPKGATYGKPVHHGVNQLKFARSLQSV
AEERAGRHCGALRVLNSYWVGEDSTYKFFEVILIDPFHKAIRRNPDTQWI
TKPVHKHREMRGLTSAGRKSRGLGKGHKFHHTIGGSRRAAWRRRNTLQLH
RYR

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

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): G2 Y4 Q8 R12 K14 Q15 W28 R31 S34 A35 P40 R41 R44 K47 R49 R50 L51 K54 A55 Q57 R65 R67 R68 R71 K72 R73 P74 K77 Y81 G82 K83 V85 H86 H87 V89 N90 Q91 K93 F94 A95 R96 L98 V101 E104 R105 R108 A112 S125 Y127 K128 F138 R144 W150 P154 H156 K157 M161 R162 S166 R169 K170 R172 K176 G177 H178 K179 H181 H182 I184 G185 G186 S187 R189 W192 R193 R195 H201 R202 Y203 R204
• Binding residue (residue number reindexed from 1): G1 Y3 Q7 R11 K13 Q14 W27 R30 S33 A34 P39 R40 R43 K46 R48 R49 L50 K53 A54 Q56 R64 R66 R67 R70 K71 R72 P73 K76 Y80 G81 K82 V84 H85 H86 V88 N89 Q90 K92 F93 A94 R95 L97 V100 E103 R104 R107 A111 S124 Y126 K127 F137 R143 W149 P153 H155 K156 M160 R161 S165 R168 K169 R171 K175 G176 H177 K178 H180 H181 I183 G184 G185 S186 R188 W191 R192 R194 H200 R201 Y202 R203

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0045471 response to ethanol
• GO:0140236 translation at presynapse
• GO:0140242 translation at postsynapse

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0031672 A band
• GO:0044391 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: Q9CZM2|RL15_MOUSE Large ribosomal subunit protein eL15 (Gene Name=Rpl15)