Structure of PDB 8hkv Chain L22P Binding Site BS01

Receptor Information

>8hkv Chain L22P (length=150) Species: 330779 (Sulfolobus acidocaldarius DSM 639)

YPILSIPEDKLAKAVIKNIDASVRDLYNVCKAIRGMNLKEAREFLNNVLE
EKEALPFWRYSHGTSHRSNISRKWKVKSGRYPKKAIKYVLKLLDNAENNA
NSKGLDIDNLKIVHIAAHKGLVLKRYMTRAFGRSTRKYKYLSHIEVILGE

Ligand information

>8hkv Chain A23S (length=2989)

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
acugagauccucugguaggggggcgcugugaugggguagaaggugggucg
ugagauccacuggacccgucacaggugcagaucccggcgguaguaacagc
gaaggggggugagaaucccccucgccggaagggcaaggguuucccggcaa
cguucgucagccgggaguuagcguccuaagguagggccuaauagguaccu
accgaaagggaaagggguuaacauuccccugccucccggguaggugcggu
aacgcaagccagacuccugacggauugggguagggagaguaggaccaccg
uccuacccaagcacucaagcccuuggagagccguaacggugagaagaggg
cgaaggugugaugggccuuccguuaggaggguucuccugaucccuagucc
ccaugaaaagggagucuggaacgaucccgggagaccguaccuagaaccga
cacuggugcccgggugagaagcccaaggcgucugagggguaacccaggcu
agggaacucggcaaauuagccccguaacuucgggagaaggggugccuauc
gugguuuaacaaagccacgauaggucgcagugaccagagggaccugacug
uuuaauaaaaacauagguccccgcuagcccgaaaggguguguacgggggc
uaaauccugccacuggugguugguuaaauccggguucaaccgggcgaagc
cccaccgaaggccggggguacccucuuaagguagccaaaugccuugccgg
guaaguuccggcgcgcaugaauggaucaacgcggucccuacugucccagc
cuggggccucgugaacgcccugagccggugcacaguccggcaucucccua
caccgagagaagaccccguggagcuucaccgcagccuggcguugucccuc
gggcguuuaugcguagaguaggugggaggggucgaaccuguccuuucggg
ggcaggggacccgaaagugaaacaccacccauggacgcucgagggacuaa
ccucucgaaagagaggaacaacgucaggugggcgguucggcuggggcggc
acucccgcgaaaagauaacacgggagcccaaaggucggcucaggcgguac
agaacgccgccguagagcgcaagggcaaaagccggccugacgugacccuu
ccaaguacggggucacgacgcgaaagcggggccuagcgaacgcucgugcc
cccacacgugggggccgggcaugacagaaaaguuaccccggggauaacag
ggucgucgcgggcgagagcucacaucgaccccgcgguuugcuacaucgau
gucggcucuucccacccuggaggugcagcugccuccaaggguagggcugc
ccgcccguuaaaggggagcgugagcuggguuuagaccgucgcgagacagg
ucggacucuaaggguagggagugcggaccgcuugaggggaaggaaccccu
aguacgagaggaacaggguuccggggccuccaguuuaccgguuguccggu
agggcaaugccgggcagccgcgcccugagggguaaccgcugaaagcaucu
aagcgggaaccccuccccuaaaagaggcggucaggcgccggggccuuccc
cuagaagaggggguugaugggguggggauguaagcuccaagguuguaaga
ccgaggaguuuaguccgccacucccaaucaggcuccccc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8hkv Cryo-EM Structures and Translocation Mechanism of Crenarchaeota Ribosome
• Resolution: 4.94 Å
• Binding residue (original residue number in PDB): K18 A19 V20 K22 N23 D25 S27 R29 R64 Y65 S66 H67 G68 H71 R72 S73 R77 W79 K80 K82 R85 Y86 K88 K89 K96 N100 N103 N104 H119 A122 H123 K124 G125 R130 R134 A135 F136 G137 R138 R141 K144
• Binding residue (residue number reindexed from 1): K13 A14 V15 K17 N18 D20 S22 R24 R59 Y60 S61 H62 G63 H66 R67 S68 R72 W74 K75 K77 R80 Y81 K83 K84 K91 N95 N98 N99 H114 A117 H118 K119 G120 R125 R129 A130 F131 G132 R133 R136 K139

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 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:8hkv, PDBe:8hkv, PDBj:8hkv
• PDBsum: 8hkv
• PubMed: 37604686
• UniProt: Q4JB45|RL22_SULAC Large ribosomal subunit protein uL22 (Gene Name=rpl22)