Structure of PDB 8g60 Chain LL Binding Site BS02

Receptor Information

>8g60 Chain LL (length=206) Species: 9606 (Homo sapiens)

APSRNGMVLKPHFHKDWQRRVATWFNQPARKIRRRKARQAKARRIAPRPA
SGPIRPIVRCPTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPR
RRNKSTESLQANVQRLKEYRSKLILFPRKPSAPKKGDSSAEELKLATQLT
GPVMPVRNVYKKEKARVITEEEKNFKAFASLRMARANARLFGIRAKRAKE
AAEQDV

Ligand information

>8g60 Chain L5 (length=3637)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgc
ggcggaucuuucccggggggaccgucccccgaccggcgaccggccgccgc
cgggcgcauuuccaccgcggcggugcgccgcgaccggcuccgggacggcu
gggaaggcccggcggggaagguggcucgggggcccccgaguguuacagcc
cccccggcagcagcacucgccgaaucccggggccgagggagcgagacccg
ucgccgcgcucuccccccugggggggccgggccaccccucccacggcgcg
accgcucgggcggacuguccccagugcgccccgggcgggucgcgccgucg
ggcccggggggccacgcgcgcguccccggggacggcggagcgagcgcacg
gggucggcggcgacgucggcuacccacccgacccgucuugaaacacggac
caaggagucuaacacgugcgcgagucgggggcucgcacgaaagccgccgu
ggcgcaaugaaggugaaggccggcgcgcucgccggccgaggugggauccc
gaggccucuccaguccgccgagggcgcaccaccggcccgucucgcccgcc
gcgccggggagguggagcacgagcgcacguguuaggacccgaaagauggu
gaacuaugccugggcagggcgaagccagaggaaacucugguggagguccg
uagcgguccugacgugcaaaucggucguccgaccuggguauaggggcgaa
agacuaaucgaaccaucuaguagcugguucccuccgaaguuucccucagg
auagcuggcgcucucgcagacccgaacgcaguuuuauccgguaaagcgaa
ugauuagaggucuuggggccgaaacgaucucaaccuauucucaaacuuua
aauggguaagaagcccggcucgcuggcguggagccgggcguggaaugcga
gugccuagugggccacuuuugguaagcagaacuggcgcugcgggaugaac
cgaacgccggguuaaggcgcccgaugccgacgcucaucagaccccagaaa
agguguugguugauauagacagcaggacgguggccauggaagucggaauc
cgcuaaggaguguguaacaacucaccugccgaaucaacuagcccugaaaa
uggauggcgcuggagcgucgggcccauacccggccgucgccggcagucga
gaguggacgggagcgcgcggacgcuacgccgcgacgaguaggagggccgc
ugcggugagccuugaagccuagggcgcgggcccggguggagccgccgcag
gugcagaucuuggugguaguagcaaauauucaaacgagaacuuugaaggc
cgaaguggagaaggguuccaugugaacagcaguugaacaugggucagucg
guccugagagaugggcgagcgccguuccgaagggacgggcgauggccucc
guugcccucggccgaucgaaagggagucggguucagauccccgaauccgg
agcggagaugggcgccgcgaggcguccagugcgguaacgcgaccgauccc
ggagaagccggcgggagccccggggagaguucucuuuucuuugugaaggg
cagggcgcccuggaauggguucgccccgagagaggggcccgugccuugga
aagcgucgcgguuccggcggcguccggugagcucucgcuggcccuugaaa
auccgggggagaggguguaaaucucgcgccgggccguacccauauccgca
gcaggucuccaaggugaacagccucuggcauguuggaacaauguagguaa
gggaagucggcaagccggauccguaacuucgggauaaggauuggcucuaa
gggcuggguagcagccgacuuagaacuggugcggaccaggggaauccgac
uguuuaauuaaaacaaagcaucgcgaaggcccgcggcggguguugacgcg
augugauuucugcccagugcucugaaugucaaagugaagaaauucaauga
agcgcggguaaacggcgggaguaacuaugacucucuuaagguagccaaau
gccucgucaucuaauuagugacgcgcaugaauggaugaacgagauuccca
cugucccuaccuacuauccagcgaaaccacagccaagggaacgggcuugg
cggaaucagcggggaaagaagacccuguugagcuugacucuagucuggca
cggugaagagacaugagagguguagaauaagugggaggcccgggccgccg
gugaaauaccacuacucugaucguuuuuucacugacccggugaggcgggg
gggcgagccccgaggggcucucgcuucuggcgccaagcgcccggcgccgg
gcgcgacccgcuccggggacagugccagguggggaguuugacuggggcgg
uacaccugucaaacgguaacgcagguguccuaaggcgagcucagggagga
cagaaaccucccguggagcagaagggcaaaagcucgcuugaucuugauuu
ucaguacgaauacagaccgugaaagcggggccucacgauccuucugaccu
uuuggguuuuaagcaggaggugucagaaaaguuaccacagggauaacugg
cuuguggcggccaagcguucauagcgacgucgcuuuuugauccuucgaug
ucggcucuuccuaucauugugaagcagaauucaccaagcguuggauuguu
cacccacuaauagggaacgugagcuggguuuagaccgucgugagacaggu
uaguuuuacccuacugaugauguguuguugccaugguaauccugcucagu
acgagaggaaccgcagguucagacauuugguguaugugcuuggcugagga
gccaauggggcgaagcuaccaucugugggauuaugacugaacgccucuaa
gucagaaucccgcccaggcggaacgauacggcagcgccgcggagccucgg
uuggccucggauagccggucccccgccgggguccggugcggagugcccuu
cguccugggaaacggggcgcggccggagaggcggccgcccccucgcccgu
cacgcaccgcacguucguggggaaccuggcgcuaaaccauucguagacga
ccugcuucugggucgggguuucguacguagcagagcagcucccucgcugc
gaucuauugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8g60 mRNA decoding in human is kinetically and structurally distinct from bacteria.
• Resolution: 2.54 Å
• Binding residue (original residue number in PDB): A2 R5 M8 L10 K11 P12 H13 F14 H15 K16 W18 Q19 R20 W25 Q28 P29 R31 K32 I33 R35 R36 K37 R39 K42 R44 R56 V59 R60 C61 P62 T63 V64 Y66 H67 K69 R71 G73 R74 L78 K88 R92 D99 P100 R101 R102 R103 K105 S106 R129 K136 R221 K226 K228 F242 R246 M247 R249 A250 N251 R253 L254 G256 R258 K260 R261
• Binding residue (residue number reindexed from 1): A1 R4 M7 L9 K10 P11 H12 F13 H14 K15 W17 Q18 R19 W24 Q27 P28 R30 K31 I32 R34 R35 K36 R38 K41 R43 R55 V58 R59 C60 P61 T62 V63 Y65 H66 K68 R70 G72 R73 L77 K87 R91 D98 P99 R100 R101 R102 K104 S105 R128 K135 R157 K162 K164 F178 R182 M183 R185 A186 N187 R189 L190 G192 R194 K196 R197

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0001824 blastocyst development
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0060348 bone development

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8g60, PDBe:8g60, PDBj:8g60
• PDBsum: 8g60
• PubMed: 37020024
• UniProt: P26373|RL13_HUMAN Large ribosomal subunit protein eL13 (Gene Name=RPL13)