Structure of PDB 8scb Chain N Binding Site BS01

Receptor Information

>8scb Chain N (length=203) Species: 9986 (Oryctolagus cuniculus)

GAYKYIQELWRKKQSDVMRFLLRVRCWQYRQLSALHRAPRPTRPDKARRL
GYKAKQGYVIYRIRVRRGGRKRPVPKGATYGKPVHHGVNQLKFARSLQSV
AEERAGRHCGALRVLNSYWVGEDSTYKFFEVILIDPFHKAIRRNPDTQWI
TKPVHKHREMRGLTSAGRKSRGLGKGHKFHHTIGGSRRAAWRRRNTLQLH
RYR

Ligand information

>8scb Chain 5 (length=3530)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggaaaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggaaau
guggcguacggaagacccaccccggcgccggggggcccaaguccuucuga
ucgaggcccagcccguggacggugugaggccgguagcggcccccggcgcg
ccgggcccgggucuucccggagucggguugcuugggaaugcagcccaaag
cgggugguaaacuccaucuaaggcuaaauaccggcacgagaccgauaguc
aacaaguaccguaagggaaaguugaaaagaacuuugaagagagaguucaa
gagggcgugaaaccguuaagagguaaacgggugggguccgcgcaguccgc
ccggaggauucaacccggcggcgcgguccggccgugccggcggggcggau
cucccgcucccgucggcgggggaccgccccccggccggcgaccggccgcc
gccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccgggacgg
cugggaaggccccggcggggaagguggcccgggggccccggguguuacag
ccccgccccggcagcagcagcucgccgaaucccggggccgagggagcgag
acccgugcgccgcgcucuccccccucgggggggccgggccaccccuccca
cggcgcgaccgcuggggcggacuguccagugcgccccgggcgggucgcgc
cgucgggcccggggggccacgcgagcgcacggggucggcggcgaugucgg
cuacccacccgacccgucuugaaacacggaccaaggagucuaacacgugc
gcgagucgggggcuacgaaagccgccguggcgcaaugaaggugaaggccg
gcggcgcgccgccggccgaggugggaucccgaggccuccaguccgccgag
ggcgcaccaccggcccgucucgcccgccgcgccggggagguggagcacga
gcgcacguguuaggacccgaaagauggugaacuaugccugggcagggcga
agccagaggaaacucugguggagguccguagcgguccugacgugcgaauc
ggucguccgaccuggguauaggggcgaaagacuaaucgaaccaucuagua
gcugguucccuccaaaguuucccucaggauagcuggcgcucuccgcaguu
uuauccgguaaagcgaaugauuagaggucuuggggccgaaacgaucucaa
ccuauucucaaacuuuaaauggguaagaagcccggcucgcugguguggag
ccgggcguggaaugcgagugccuagugggccacuuuugguaagcagaacu
ggcgcugcgggaugaaccgaacgccggguuaaggcgcccgaugccgacgc
ucaucagaccccagaaaagguguugguugauauagacagcaggacggugg
ccauggaagucggaauccgcuaaggaguguguaacaacucaccugccgaa
ucaacuagcccugaaaauggauggcgcuggagcgucgggcccauacccgg
ccgucgcuggcagucggcagagcgagaaagagaguggcgcggacgcuacg
ccgcgacgaguaggagggccgcugcggugagccuugaagccuagggcgcg
ggcccggguggagccgccgcaggugcagaucuuggugguaguagcaaaua
uucaaacgagaacuuugaaggccgaaguggagaaggguuccaugugaaca
gcaguugaacaugggucagucgguccugagagaugggcgagcgccguucc
gaagggacgggcgauggccuccguugcccucagccgaucgaaagggaguc
ggguucagauccccgaauccggaguggcggagaugggcgccgcgaggcgu
ccagugcgguaacgcgaccgaucccggagaagccggcgggagccccgggg
agaguucucuuuucuuugugaagggcagggcgcccuggaauggguucgcc
ccgagagaggggcccgugccuuggaaagcgucgcgguuccggcggcgucc
ggugagcucucgcuggcccuugaaaauccgggggagaggguguaaaucuc
gcgccgggccguacccauauccgcagcaggucuccaaggugaacagccuc
uggcauguuggaacaauguagguaagggaagucggcaagccggauccgua
acuucgggauaaggauuggcucuaagggcuggcagccgacuuagaacugg
ugcggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaagg
cccgcggcggguguugacgcgaugugauuucugcccagugcucugaaugu
caaagugaagaaauucaaugaagcgcggguaaacggcgggaguaacuaug
acucucuuaagguagccaaaugccucgucaucuaauuagugacgcgcaug
aauggaugaacgagauucccacugucccuaccuacuauccagcgaaacca
cagccaagggaacgggcuuggcggaaucagcggggaaagaagacccuguu
gagcuugacucuagucuggcacggugaagagacguuuuuucacugacccg
gugaggcgggggggcgagccgggcucucgcuucuggcgccaagcgcccgg
ccggccgggcgcgacccgcuccggggacagugccagguggggaguuugac
uggggcgguacaccugucaaacgguaacgcagguguccuaaggcgagcuc
agggaggacagaaaccucccguggagcagaagggcaaaagcucgcuugau
cuugauuuucaguacgaauacagaccgugaaagcggggccucacgauccu
ucugaccuuuuggguuuuaagcaggaggugucagaaaaguuaccacaggg
auaacuggcuuguggcggccaagcguucauagcgacgucgcuuuuugauc
cuucgaugucggcucuuccuaucauugugaagcagaauucaccaagcguu
ggauuguucacccacuaauagggaacgugagcuggguuuagaccgucgug
agacagguuaguuuuacccuacugaugauguguuguugccaugguaaucc
ugcucaguacgagaggaaccgcagguucagacauuugguguaugugcuug
gcugaggagccaauggggcgaagcuaccaucugugggauuaugacugaac
gccucuaagucagaaucccgcccaggcggaacgauagcgccggagccucg
guuggccucggauagccggucccccgccgggguccggugcggagagcccu
ucgucccgggaaacgggcggccggaaagggggccgcccucucgcccguca
cgcaccgcacguucguggggaaccuggcgcuaaaccauucguagacgacc
ugcuucugggucgggguuucguacguagcagagcagcugcugcgaucuau
ugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8scb Structure and consequences of eRF1 glued to the ribosomal decoding center
• Resolution: 2.5 Å
• Binding residue (original residue number in PDB): G2 Y4 K5 Q8 R12 K13 K14 Q15 R24 W28 R31 Q32 P40 R41 R44 K47 R49 R50 L51 K54 A55 K56 Q57 R65 R67 R68 G69 G70 R71 K72 P74 V75 K77 G78 Y81 G82 K83 P84 V85 H86 H87 N90 Q91 K93 F94 A95 R96 S97 L98 E104 R105 R108 A112 W120 D124 S125 Y127 K128 F138 K140 A141 R144 W150 P154 V155 H156 K157 H158 M161 R162 L164 S166 R169 K170 S171 R172 K176 G177 H178 K179 H181 H182 I184 G185 G186 S187 W192 R193 R194 R195 Q199 H201 R202 R204
• Binding residue (residue number reindexed from 1): G1 Y3 K4 Q7 R11 K12 K13 Q14 R23 W27 R30 Q31 P39 R40 R43 K46 R48 R49 L50 K53 A54 K55 Q56 R64 R66 R67 G68 G69 R70 K71 P73 V74 K76 G77 Y80 G81 K82 P83 V84 H85 H86 N89 Q90 K92 F93 A94 R95 S96 L97 E103 R104 R107 A111 W119 D123 S124 Y126 K127 F137 K139 A140 R143 W149 P153 V154 H155 K156 H157 M160 R161 L163 S165 R168 K169 S170 R171 K175 G176 H177 K178 H180 H181 I183 G184 G185 S186 W191 R192 R193 R194 Q198 H200 R201 R203

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0044391 ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8scb, PDBe:8scb, PDBj:8scb
• PDBsum: 8scb
• PubMed: 38172604
• UniProt: G1T0C1|RL15_RABIT Large ribosomal subunit protein eL15 (Gene Name=RPL15)