Structure of PDB 8hky Chain AL4P Binding Site BS01

Receptor Information

>8hky Chain AL4P (length=251) Species: 330779 (Sulfolobus acidocaldarius DSM 639)

KVSVLDLKGNQLEEIELPLFFSYPVRKDLIRRVFLSEFTKSLQPKGRDPL
AGKRTSALSFGINLGIARVPRVKGSGEAALAPNTVGGRLAFPPTTEKRLV
EEVNLKEKKLGIISALAATADPNFVKARGHRFTSNNVPIILVDDFENISK
AKEIMDILKSIGVVDDIKRVKESKGVRAGKGKMRGRRYQIAKGPLIVVSN
HKSPVVESASNIPGVNVVSANLVSVIHLAPGGHPGRLTIYTKSSINILRQ
R

Ligand information

>8hky Chain A23S (length=2996)

aagccucccgguggauggcucggcucgggcaccgaagaagggcgcggcaa
gcagcgaaaugcucgggugaggcgcaagcagccguugaccccgagguccc
cuaaugggauauccugccggguuuccggcgcccgguuuauaacugggugg
gaaccccccgaacggaaacaucuuaguagggggaggaaaagaaaucaauu
gagauccccugaguaggggcgaccgaaagggggacagcccaaacuaaacc
ugccgaugauaagucgguggggaugugguguuacgaccucuagccugagg
uugaccucggcuuuccuaaccuaucuagccgaacuccccuggaacggggg
gccauagagggugaaagccccguaggcuaaagauagguggaaaguggcua
gagguagaguaccauccccugguuugggggugggaaguuaggggacacgu
gccucuaaggcuaaauaugucccgagaccgauagcaaacuaaguaccgug
agggaaagcugaaaagaaccccggaagggggagugcaaagagccugaaac
cgggugguuauacaggguguggcucgaaagaagugaacccuuccgaagga
aaggggcgcaagcccuuaguacgaggaagggcgaucggggucacgccuuu
cgucuugaaacacgggccggggaguucacaucaguggcgagcuuaaggag
auuaucuccgaaggcauagggaaaccaagugcccgcagccuaguuucuag
gcgaggggcagggucugucagggccugaagccacugaugugaggcuagaa
accgggcgaucuaguccggggcaggcugaaggugggggaaaccccacugg
agggccgaauagggguucugacgugcaauucguucccuugaccucggacu
aggggcaaaagaccaaucuagcccggugauagcuaguuccccccgaaaug
cguccuagcgcagccucccuaaaggcagcucgcgggguagagugacagau
cgggggcuccaggcgccuggggcuuccggucuaacuccgaacccacgagc
gccgaagaaggggggagugggucacucggcguaagguuggguggcaaaag
gggaacaacccagaccuggguuaaggccccaaagucccggcuaagugcca
acgaaaaggcgucuccagccuuagacagcgggaaggugggcccagcagca
gccauccucuaaggagugcguaacagcucacccgccgaggcuggaggccc
uaaagauuggucggggcucaagccgggcgccgagacccaggagggggucu
cuacugagauccucugguaggggggcgcugugaugggguagaaggugggu
cgugagauccacuggacccgucacaggugcagaucccggcgguaguaaca
gcgaaggggggugagaaucccccucgccggaagggcaaggguuucccggc
aacguucgucagccgggaguuagccuccuaagguagggccuaauagguac
cuaccgaaagggaaagggguuaacauuccccugccucccggguaggugcg
guaacgcaagccagacuccugacggauugggguagggagaguaggaccac
cguccuacccaagcacucaagcccuuggagagccguaacggugagaagag
ggcgaaggugugaugggccuuccguuaggaggguucuccugaucccuagu
ccccaugaaaagggagucuggaacgaucccgggagaccguaccuagaacc
gacacuggugcccgggugagaagcccaaggcgucugagggguaacccagg
cuagggaacucggcaaauuagccccguaacuucgggagaaggggugccua
ucgugguuuaacaaagccacgauaggucgcagugaccagagggaccugac
uguuuaauaaaaacauagguccccgcuagcccgaaaggguguguacgggg
gcuaaauccuggccacuggugguugaaauccggguucaaccgggcgaagc
cccaccgaaggccggggguaacucugacccucuuaagguagccaaaugcc
uugccggguaaguuccggcgcgcaugaauggaucaacgcggucccuacug
ucccagccuggggccucgugaacgcccugagccggugcacaguccggcau
cucccuacaccgagagaagaccccguggagcuucaccgcagccuggcguu
gucccucgggcguuuaugcguagaguaggugggaggggucgaaccugucc
uuucgggggcaggggacccgaaagugaaacaccacccauggacgcucgag
ggacuaaccucucgaaagagaggaacaacgucaggugggcgguucggcug
gggcggcacucccgcgaaaagauaacacgggagcccaaaggucggcucag
gcgguacagaacgccgccguagagcgcaagggcaaaagccggccugacgu
gacccuuccaaguacggggucacgacgcgaaagcggggccuagcgaacgc
ucgugcccccacacgugggggccgggcaugacagaaaaguuaccccgggg
auaacagggucgucgcgggcgagagcucacaucgaccccgcgguuugcua
caucgaugucggcucuucccacccuggaggugcagcugccuccaagggua
gggcugcccgcccguuaaaggggagcgugagcuggguuuagaccgucgcg
agacaggucggacucuaaggguagggagugcggaccgcuugaggggaagg
aaccccuaguacgagaggaacaggguuccggggccuccaguuuaccgguu
guccgguagggcaaugccgggcagccgcgcccugagggguaaccgcugaa
agcaucuaagcgggaaccccuccccuaaaagaggcggucaggcgccgggg
ccuuccccuagaagaggggguugaugggguggggauguaagcuccaaggu
uguaagaccgaggaguuuaguccgccacucccaaucaggcuccccc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8hky Cryo-EM Structures and Translocation Mechanism of Crenarchaeota Ribosome
• Resolution: 4.45 Å
• Binding residue (original residue number in PDB): V33 R34 R39 R40 E45 F46 K48 L50 Q51 P52 K53 G54 R55 D56 A59 G60 R62 T63 S64 I70 N71 G73 A75 R76 V77 P78 R79 N91 V93 G94 R96 L97 F99 E104 K105 R106 E109 E110 N112 L113 K114 E115 K116 F132 G137 K158 A159 K160 M163 R177 V184 R185 K188 K190 M191 R192 R194 R195 Y196 Q197 A199 K200 H209 E215 S218 N219 N229 L230 S232 H235
• Binding residue (residue number reindexed from 1): V25 R26 R31 R32 E37 F38 K40 L42 Q43 P44 K45 G46 R47 D48 A51 G52 R54 T55 S56 I62 N63 G65 A67 R68 V69 P70 R71 N83 V85 G86 R88 L89 F91 E96 K97 R98 E101 E102 N104 L105 K106 E107 K108 F124 G129 K150 A151 K152 M155 R169 V176 R177 K180 K182 M183 R184 R186 R187 Y188 Q189 A191 K192 H201 E207 S210 N211 N221 L222 S224 H227

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:8hky, PDBe:8hky, PDBj:8hky
• PDBsum: 8hky
• PubMed: 37604686
• UniProt: Q4JB41|RL4_SULAC Large ribosomal subunit protein uL4 (Gene Name=rpl4)