Structure of PDB 8hku Chain L13P Binding Site BS01

Receptor Information

>8hku Chain L13P (length=140) Species: 330779 (Sulfolobus acidocaldarius DSM 639)

VIVDATNQILGRMSTHIAKLLKSGKKVYVVNAEKAIISGPRSRVLEGYSL
LFTVKTMQNPYRQGIRRPRNPINIVKRTVRGMLPKNKLGKQIYRNLKAYI
GIPKELEGKSMIRFDDADVSRLKGKYITVAELSRLLGGLK

Ligand information

>8hku Chain A23S (length=2995)

aagccucccgguggauggcucggcucgggcaccgaagaagggcgcggcaa
gcagcgaaaugcucgggugaggcgcaagcagccguugaccccgagguccc
cuaaugggauauccugccggguuuccggcucccgguuuauaacugggugg
gaaccccccgaacggaaacaucuuaguagggggaggaaaagaaaucaauu
gagauccccugaguaggggcgaccgaaagggggacagcccaaacuaaacc
ugccgaugauaagucgguggggaugugguguuacgaccucuagccugagg
uugaccucggcuuuccuaaccuaucuagccgaacuccccuggaacggggg
gccauagagggugaaagccccguaggcuaaagauagguggaaaguggcua
gagguagaguaccauccccugguuugggggugggaaguuaggggacacgu
gccucuaaggcuaaauaugucccgagaccgauagcaaacuaaguaccgug
agggaaagcugaaaagaaccccggaagggggagugcaaagagccugaaac
cgggugguuauacaggguguggcucgaaagaagugaacccuuccgaagga
aaggggcgcaagcccuuaguacgaggaagggcgaucggggucacgccuuu
cgucuugaaacacgggccggggaguucacaucaguggcgagcuuaaggag
auuaucuccgaaggcauagggaaaccaagugcccgcagccuaguuucuag
gcgaggggcagggucugucagggccugaagccacugaugugaggcuagaa
accgggcgaucuaguccggggcaggcugaaggugggggaaaccccacugg
agggccgaauagggguucugacgugcaauucguucccuugaccucggacu
aggggcaaaagaccaaucuagcccggugauagcuaguuccccccgaaaug
cguccuagcgcagccucccuaaaggcagcucgcgggguagagugacagau
cgggggcuccaggcgccuggggcuuccggucuaacuccgaacccacgagc
gccgaagaaggggggagugggucacucggcguaagguuggguggcaaaag
gggaacaacccagaccuggguuaaggccccaaagucccggcuaagugcca
acgaaaaggcgucuccagccuuagacagcgggaaggugggcccagcagca
gccauccucuaaggagugcguaacagcucacccgccgaggcuggaggccc
uaaagauuggucggggcucaagccgggcgccgagacccaggagggggucu
cuacuagagauccucugguaggggggcgcugugaugggguagaagguggg
ucgugagauccacuggacccgucacaggugcagaucccggcgguaguaac
agcgaaggggggugagaaucccccucgccggaagggcaaggguuucccgg
caacguucgucagccgggaguuagccgguccuaagguagggccuaauagg
uaccuaccgaaagggaaagggguuaacauuccccugccucccggguaggu
gcgguaacgcaagccagacuccugacggauugggguagggagaguaggac
caccguccuacccaagcacucaagcccuuggagagccguaacggugagaa
gagggcgaaggugugaugggccuuccguuaggaggguucuccugaucccu
aguccccaugaaaagggagucuggaacgaucccgggagaccguaccuaga
accgacacuggugccccggugagaagcccaaggcgucugagggguaaccc
aggcuagggaacucggcaaauuagccccguaacuucgggagaaggggugc
cuaucgugguuuaacaaagccacgauaggucgcagugaccagagggaccu
gacuguuuaauaaaaacauagguccccgcuagcccgaaaggguguguacg
ggggcuaaauccuggccacuggugguugguuaaauccggguucaaccggg
cgaagccccaccgaaggccggggguacccucuuaagguagccaaaugccu
ugccggguaaguuccggcgcgcaugaauggaucaacgcggucccuacugu
cccagccuggggccucgugaacgcccugagccggugcacaguccggcauc
ucccuacaccgagagaagaccccguggagcuucaccgcagccuggcguug
ucccucgggcguuuaugcguagaguaggugggaggggucgaaccuguccu
uucgggggcaggggacccgaaagugaaacaccacccauggacgcucgagg
gacuaaccucucgaaagagaggaacaacgucaggugggcgguucggcugg
ggcggcacucccgcgaaaagauaacacgggagcccaaaggucggcucagg
cgguacagaacgccgccguagagcgcaagggcaaaagccggccugacgug
acccuuccaaguacggggucacgacgcgaaagcggggccuagcgaacgcu
cgugcccccacacgugggggccgggcaugacagaaaaguuaccccgggga
uaacagggucgucgcgggcgagagcucacaucgaccccgcgguuugcuac
aucgaugucggcucuucccacccuggaggugcagcugccuccaaggguag
ggcugcccgcccguuaaaggggagcgugagcuggguuuagaccgucgcga
gacaggucggacucuaaggguagggagugcggaccgcuugaggggaagga
accccuaguacgagaggaacaggguuccggggccuccaguuuaccgguug
uccgguagggcaaugccgggcagccgcgcccugagggguaaccgcugaaa
gcaucuaagcgggaaccccuccccuaaaagaggcggucaggcgccggggc
cuuccccuagaagaggggguugaugggguggggauguaagcuccaagguu
guaagaccgaggaguuuaguccgccacucccaaucaggcuccccc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8hku Cryo-EM Structures and Translocation Mechanism of Crenarchaeota Ribosome
• Resolution: 2.72 Å
• Binding residue (original residue number in PDB): G18 R19 T22 S45 R50 L57 L58 F59 T60 V61 K62 T63 M64 Q65 N66 P67 Y68 R69 Q70 I72 R73 R74 R76 N80 K83 R84 T85 R87 G88 M89 P91 N93 K94 L95 R101 K104 A105 Y106 D123 L129 K130
• Binding residue (residue number reindexed from 1): G11 R12 T15 S38 R43 L50 L51 F52 T53 V54 K55 T56 M57 Q58 N59 P60 Y61 R62 Q63 I65 R66 R67 R69 N73 K76 R77 T78 R80 G81 M82 P84 N86 K87 L88 R94 K97 A98 Y99 D116 L122 K123

Gene Ontology

Molecular Function

• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation
• GO:0017148 negative regulation of translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8hku, PDBe:8hku, PDBj:8hku
• PDBsum: 8hku
• PubMed: 37604686
• UniProt: P39473|RL13_SULAC Large ribosomal subunit protein uL13 (Gene Name=rpl13)