Structure of PDB 8g61 Chain SJ Binding Site BS01

Receptor Information

>8g61 Chain SJ (length=185) Species: 9606 (Homo sapiens)

PVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLA
KIRKAARELLTLDEKDPRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLK
IEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVVNIPSFIVRL
DSQKHIDFSLRSPYGGGRPGRVKRKNAKKGQGGAG

Ligand information

>8g61 Chain S2 (length=1682)

uaccugguugauccugccaguagcauaugcuugucucaaagauuaagcca
ugcaugucuaaguacgcacggccgguacagugaaacugcgaauggcucau
uaaaucaguuaugguuccuuuggucgcucgccacuuggauaacuguggua
auucuagagcuaauacaugccgacgggcgcugacccccuucgcggggggg
augcgugcauuuaucaguggugacucuagauaaccucgggccgaucgcac
gccccccguggcggcgacgacccauucgaacgucugcccuaucaacuuuc
gaugguagucgccgugccuaccauggugaccacgggugacggggaaucag
gguucgauuccggagagggagccugagaaacggcuaccacauccaaggaa
ggcagcaggcgcgcaaauuacccacucccgacccggggagguagugacga
aaaauaacaauacaggacucuuucgaggcccuguaauuggaaugagucca
cuuuaaauccuuuaacgaggauccauuggagggcaagucuggugccagca
gccgcgguaauuccagcuccaauagcguauauuaaaguugcugcaguuaa
aaagcucguaguuggaucuuguuacuuugaaaaaauuagaguguucaaag
caggcccgagccgccuggauaccgcagcuaggaauaauggaauaggaccg
cgguucuauuuuguugguuuucggaacugaggccaugauuaagagggacg
gccgggggcauucguauugcgccgcuagaggugaaauucuuggaccggcg
caagacggaccagagcgaaagcauuugccaagaauguuuucauuaaucaa
gaacgaaagucggagguucgaagacgaucagauaccgucguaguuccgac
cauaaacgaugccgaccggcgaugcggcggcguuauucccaugacccgcc
gggcagcuuccgggaaaccaaagucuuuggguuccggggggaguaugguu
gcaaagcugaaacuuaaaggaauugacggaagggcaccaccaggagugga
gccugcggcuuaauuugacucaacacgggaaaccucacccggcccggaca
cggacaggauugacagauugauagcucuuucucgauuccguggguggugg
ugcauggccguucuuaguugguggagcgauuugucugguuaauuccgaua
acgaacgagacucuggcaugcuaacuaguuacgcgacccccgagcggucg
gcgucccccaacuucuuagagggacaaguggcguucagccacccgagauu
gagcaauaacaggucugugaugcccuuagauguccggggcugcacgcgcg
cuacacugacuggcucagcgugugccuacccuacgccggcaggcgcgggu
aacccguugaaccccauucgugauggggaucggggauugcaauuauuccc
caugaacgaggaauucccaguaagugcgggucauaagcuugcguugauua
agucccugcccuuuguacacaccgcccgucgcuacuaccgauuggauggu
uuagugaggcccucggaucggccccgccggggugcccuggcggagcgcug
agaagacggucgaacuugacuaucuagaggaaguaaaagucguaacaagg
uuuccguaggugaaccugcggaaggaucauua

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8g61 mRNA decoding in human is kinetically and structurally distinct from bacteria.
• Resolution: 2.94 Å
• Binding residue (original residue number in PDB): P2 V3 R5 S6 W7 V8 C9 R10 K11 T12 Y13 T15 R17 R18 P19 F20 R38 N39 K40 R41 R45 R58 F72 A76 R79 R80 R83 K121 S122 H125 R127 V128 R131 Q132 R133 H134 Q140 V142 N143 I144 S146 F147 I148 R150 S153 P164 Y165 R169 G171 R172 V173 K174 K176 N177
• Binding residue (residue number reindexed from 1): P1 V2 R4 S5 W6 V7 C8 R9 K10 T11 Y12 T14 R16 R17 P18 F19 R37 N38 K39 R40 R44 R57 F71 A75 R78 R79 R82 K120 S121 H124 R126 V127 R130 Q131 R132 H133 Q139 V141 N142 I143 S145 F146 I147 R149 S152 P163 Y164 R168 G170 R171 V172 K173 K175 N176

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding
• GO:0045182 translation regulator activity

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0006417 regulation of translation
• GO:0008284 positive regulation of cell population proliferation
• GO:0042274 ribosomal small subunit biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0015935 small ribosomal subunit
• GO:0016020 membrane
• GO:0022626 cytosolic ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0032040 small-subunit processome
• GO:0043226 organelle
• GO:0045202 synapse
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8g61, PDBe:8g61, PDBj:8g61
• PDBsum: 8g61
• PubMed: 37020024
• UniProt: P46781|RS9_HUMAN Small ribosomal subunit protein uS4 (Gene Name=RPS9)