Structure of PDB 8d8j Chain E Binding Site BS01

Receptor Information

>8d8j Chain E (length=168) Species: 4932 (Saccharomyces cerevisiae)

YITRKLTMKPLVMKRVSNQTGKGKIASFYALVVVGDKNGMVGLGEGKSRE
EMSKAIFKAHWDAVRNLKEIPRYENRTIYGDIDFRYHGVKLHLRSAKPGF
GLRVNHVIFEICECAGIKDLSGKVYKSRNDMNIAKGTIEAFTKAQKTLDE
VALGRGKKLVDVRKVYYS

Ligand information

>8d8j Chain a (length=1183)

uuuuauauauauauaauaaggaaaaguauuuauaagaauaugauguuggu
ucagauuaagcgcuaaauaaggacaugacacaugcgaaucauacguuuau
uauugagauaauaaauaugugguguaaacgugaguaauuuuauuaggaau
uaaugaacuauagaauaagcuaaauacuuaauauuauauaaaaauaauuu
auauaauaaaaaggauauauauauauauauuuaucuauagucaagccaau
aaugguuuagguaguagguuuauuaagaguuaaaccuagccaacgaucca
uaaucgauaaugaaaguuagaacgaucacguugacucugaaauauaguca
auaucuauaagauacagcagugaggaauauuggacaaugaucgaaagauu
gauccaguuacuuauuaggaugauauauauauauauauaaauugauuaaa
aauaaaauccauaaauaauuaaaauaaugauauuaauuaccauauauuua
uauggauauauauauauuuuaauaguccugacuaauauuugugccagcag
ucgcgguaacacaaagagggcgagcguuaaucauaaugguuuaaaggauc
cguagaaugaauuauauauaauuuagaguuaauaaaauauaauuaaagaa
uuauaauaaauuauaagacuaauauaugugaaaauauuaauuaaauauua
acugacauugagggauuaaaacuagagucuaguaguaugaauacaauuau
uuauaauauauauauaaauaauaaaugaaaaugaaaguauuccaccugaa
gaguacguuagcaauaaugaaacucaaaacaauagacgguuacagacuua
agcaguggagcauguuauuuaauucuaccauauuuugaauauuauaauaa
uuauaauuauuauauuacaggcguuacauuguuaaugauccuuauaauau
ggguaauagacgugcuauaauaaaaugauaaaaaacauuuuaaauaugaa
aaaagaauugcuaguaauacguaaauuaguauguuacggugaauauucua
acuguuucgcacuaaucacucaucacgcguugaaacauauuauuaucuua
uuauuuauauaauauuuuuuaauaaauauuauuaauuuauauuuauuuau
aucagaaauaauaugaauuaaugcgaaguugaa

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8d8j Principles of mitoribosomal small subunit assembly in eukaryotes.
• Resolution: 3.8 Å
• Binding residue (original residue number in PDB): K152 V154 S155 N156 Q157 G159 K162 R223 H225 G226 K228 H230 R232 A234 K235 F238 R241 V242 N243 H244 G260 K261 Y263 K264 S265 R266 N267 N270 K302 Y304 Y305
• Binding residue (residue number reindexed from 1): K14 V16 S17 N18 Q19 G21 K24 R85 H87 G88 K90 H92 R94 A96 K97 F100 R103 V104 N105 H106 G122 K123 Y125 K126 S127 R128 N129 N132 K164 Y166 Y167

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation
• GO:0032543 mitochondrial translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005739 mitochondrion
• GO:0005743 mitochondrial inner membrane
• GO:0005763 mitochondrial small ribosomal subunit
• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8d8j, PDBe:8d8j, PDBj:8d8j
• PDBsum: 8d8j
• PubMed: 36482135
• UniProt: P33759|RT05_YEAST Small ribosomal subunit protein uS5m (Gene Name=MRPS5)