Structure of PDB 8hl5 Chain AL4P Binding Site BS01

Receptor Information

>8hl5 Chain AL4P (length=251) Species: 330779 (Sulfolobus acidocaldarius DSM 639)

KVSVLDLKGNQLEEIELPLFFSYPVRKDLIRRVFLSEFTKSLQPKGRDPL
AGKRTSALSFGINLGIARVPRVKGSGEAALAPNTVGGRLAFPPTTEKRLV
EEVNLKEKKLGIISALAATADPNFVKARGHRFTSNNVPIILVDDFENISK
AKEIMDILKSIGVVDDIKRVKESKGVRAGKGKMRGRRYQIAKGPLIVVSN
HKSPVVESASNIPGVNVVSANLVSVIHLAPGGHPGRLTIYTKSSINILRQ
R

Ligand information

>8hl5 Chain A23S (length=2991)

aagccucccgguggauggcucggcucgggcaccgaagaagggcgcggcaa
gcagcgaaaugcucgggugaggcgcaagcagccguugaccccgagguccc
cuaaugggauauccugccggguuccggcgcccgguuuauaacuggguggg
aaccccccgaacggaaacaucuuaguagggggaggaaaagaaaucaauug
agauccccugaguaggggcgaccgaaagggggacagcccaaacuaaaccu
gccgaugauaagucgguggggaugugguguuacgaccucuagccugaggu
ugaccucggcuuuccuaaccuaucuagccgaacuccccuggaacgggggg
ccauagagggugaaagccccguaggcuaaagauagguggaaaguggcuag
agguagaguaccauccccugguuugggggugggaaguuaggggacacgug
ccucuaaggcuaaauaugucccgagaccgauagcaaacuaaguaccguga
gggaaagcugaaaagaaccccggaagggggagugcaaagagccugaaacc
gggugguuauacaggguguggcucgaaagaagugaacccuuccgaaggaa
aggggcgcaagcccuuaguacgaggaagggcgaucggggucacgccuuuc
gucuugaaacacgggccggggaguucacaucaguggcgagcuuaaggaga
uuaucuccgaaggcauagggaaaccaagugcccgcagccuaguuucuagg
cgaggggcagggucugucagggccugaagccacugaugugaggcuagaaa
ccgggcgaucuaguccggggcaggcugaaggugggggaaaccccacugga
gggccgaauagggguucugacgugcaauucguucccuugaccucggacua
ggggcaaaagaccaaucuagcccggugauagcuaguuccccccgaaaugc
guccuagcgcagccucccuaaaggcagcucgcgggguagagugacagauc
gggggcuccaggcgccuggggcuuccggucuaacuccgaacccacgagcg
ccgaagaaggggggagugggucacucggcguaagguuggguggcaaaagg
ggaacaacccagaccuggguuaaggccccaaagucccggcuaagugccaa
cgaaaaggcgucuccagccuuagacagcgggaaggugggcccagcagcag
ccauccucuaaggagugcguaacagcucacccgccgaggcuggaggcccu
aaagauuggucggggcucaagccgggcgccgagacccaggagggggucuc
uacugagauccucugguaggggggcgcugugaugggguagaagguggguc
gugagauccacuggacccgucacaggugcagaucccggcgguaguaacag
cgaaggggggugagaaucccccucgccggaagggcaaggguuucccggca
acguucgucagccgggaguuagcguccuaagguagggccuaauagguacc
uaccgaaagggaaagggguuaacauuccccugccucccggguaggugcgg
uaacgcaagccagacuccugacggauugggguagggagaguaggaccacc
guccuacccaagcacucaagcccuuggagagccguaacggugagaagagg
gcgaaggugugaugggccuuccguuaggaggguucuccugaucccuaguc
cccaugaaaagggagucuggaacgaucccgggagaccguaccuagaaccg
acacuggugcccgggugagaagcccaaggcgucugagggguaacccaggc
uagggaacucggcaaauuagccccguaacuucgggagaaggggugccuau
cgugguuuaacaaagccacgauaggucgcagugaccagagggaccugacu
guuuaauaaaaacauagguccccgcuagcccgaaaggguguguacggggg
cuaaauccuggccacuggugguugguuaaauccggguucaaccgggcgaa
gccccaccgaaggccggggguacccucuuaagguagccaaaugccuugcc
ggguaaguuccggcgcgcaugaauggaucaacgcggucccuacuguccca
gccuggggccucgugaacgcccugagccggugcacaguccggcaucuccc
uacaccgagagaagaccccguggagcuucaccgcagccuggcguuguccc
ucgggcguuuaugcguagaguaggugggaggggucgaaccuguccuuucg
ggggcaggggacccgaaagugaaacaccacccauggacgcucgagggacu
aaccucucgaaagagaggaacaacgucaggugggcgguucggcuggggcg
gcacucccgcgaaaagauaacacgggagcccaaaggucggcucaggcggu
acagaacgccgccguagagcgcaagggcaaaagccggccugacgugaccc
uuccaaguacggggucacgacgcgaaagcggggccuagcgaacgcucgug
cccccacacgugggggccgggcaugacagaaaaguuaccccggggauaac
agggucgucgcgggcgagagcucacaucgaccccgcgguuugcuacaucg
augucggcucuucccacccuggaggugcagcugccuccaaggguagggcu
gcccgcccguuaaaggggagcgugagcuggguuuagaccgucgcgagaca
ggucggacucuaaggguagggagugcggaccgcuugaggggaaggaaccc
cuaguacgagaggaacaggguuccggggccuccaguuuaccgguuguccg
guagggcaaugccgggcagccgcgcccugagggguaaccgcugaaagcau
cuaagcgggaaccccuccccuaaaagaggcggucaggcgccggggccuuc
cccuagaagaggggguugaugggguggggauguaagcuccaagguuguaa
gaccgaggaguuuaguccgccacucccaaucaggcuccccc

<.<<<.<<<<<<.....<<..<<<<<<<<<<<<.....<<<<<<<.((..
((.>>>.....<<<<<<...<<<))..)).>>>......>>>>>>...>>
>>...<<<....>>><<<<<<.>>>>>><<<<<<<<...>>>>>>>>>>.
..<<<<<<....<<<....>>>.....>>>>>.>.........<<....>
>..<<<<<<.....<<.....>>....>>>>>>..<<<...<<<...<<<
<<<<<<.....>>>>>>>>>.....>>>......<<<<<<<<<<<<<<<<
..>>>>>><<<<<<<...<<<<<<<.<<<.....<<<<......>>>>.(
(......<<<.....))>>>...>>>...>>>>>>>.>>>>>>>>>>>>>
>>>>......<<<<<<<<......>>>>>>>>.......<<<<.((((((
>>>>...>>>......>>.>>>>>>.>>................<<....
>>....>>.........<<<<.....>>>>.................>>>
>>>.>>>>......<<<<<<<<<<....<<......<<<<<<<...<...
.<<<<<....>>>>>.....>..>>>>>>>...>>.>>>>>>>>>>..<<
<<........>>>><<<<<<...<<<<<<<<<<<<<<..<<<...<<<<<
...>>>>>...>>>...<<....>>...<<<<<...<<<<.......>>>
>...>>>>><<<<<<....>>>>>>...>>>>>>>>>>>>>>.<<<<..<
<<<<<<.....<<<<<<<<<..<<<....<<<<<<<....>>>>>>>...
..>>>....<<<<<....<<........>>..>>>>>...>>>>>>>>>.
..<<.......>>......>>>>>>...>..>>>>..<<<<<<....<<<
<<....>>>>><<<<<<<<...<<<.<<<<<.<<<...<<<....<<<<<
<<<<<<<<<<<<<>>>>>>>>>>>>>>>>>>..>>.>...>>>.>>>>>>
>>......>>>>>>.>>..<<<<<<.<<<.....>>>.>>>>>>....<<
<......>>>...<<<<<<<...<<<(((.....<<<<<<.....<<...
.....<<<.<<<<<<<<<<.......<<<<..<<....<<.........>
>....>>.........<<......>>....>>>>...>>>>>>>>>>>>>
...........)))>>....>>>>>>.>>>...>>>>>>><<<<<<<<<<
....>>>>>>>>>>....>>>>>><<<<<<<<<.<<<.....<<<<<<<<
....>>>>>>>>...>>>>>>>>>>.>>.....>>>>>><......<<..
....<<<<<<.......>>>>>><<<<....<<<<..<<...<<<<<<..
..<.....>..>>>>>>....<.{<<<...<<<<<<.<<.....>>..>>
>>>>....>>>..<<<<<........>>>>>.><<<<<<<<.....<<<.
...>>>...<<<<<<<<<<...<<<<<<<<<..<<<<<<<<<<<<<.[[[
>>>>>>>....<<<<.<..<<<<<<.....<<<<...>>>>.....>>>>
>>...>>>>>.....<<<<<<<....>>>>>>>>>>>>>...>>>>>>>>
>.........>>>>>>>>>>......>>>>>>>>.}....>>.....<<.
.....>>.>>>><<<<.....>>>>..>>>>...<<<<.....<<<<<<<
<.<<...............<<<<<.....<..>......>>>>><<<<<<
<<<<<<<......>>>>>>>>>>>>>............<<<<<<<<<..<
<<.........>>>..<<<<<<<....<<<<....>>>>......>>>>>
>>..<<<<.<<<..<<<<<<<..<<<<...<<<<<......>>>>>...>
>>>>>>>>..>>>>><<<<<..>>>>>....................<<<
<<<.....>>>>>>..........>>>>...>>.>>>>>>>.....>>.>
>>>>>>>.>>>>>>.....>.....<<<<<........>>>>>..<<<<<
<<<.<<..<<......<<<<.<<<<<<..<<<<<.<<<<<<<<<.<<<<<
<<<<<<<<<.<<<.........<<<<<..<<<...........<.<....
.>.>.......>>>............>>>>>>>>.>>>>>>>>>>>>>>.
..<<<<<<....>>>>>>....>>>>>>>>>..>>>>>...<<<.....>
>>..<<<<<.............>>>>>.(<<...<<<<<<<...<<<<<<
.......>>>>>>.....<<)..(((>>....>>>>>>>...<<<<<<<<
<.........>>>>>>>>>.<<<....>>>.>>))).......<<<<<.<
<<<<..))))))>>>>>>>>>>..........>>>>..>>>>>>......
.<<<<...<<<<<<...<<.......>>...>>>>>>....>>>.>....
.....<<<.<.<<<<..<<<<<<<<<......>>>>>>>..>>..<<<<.
....>>>>......>>>>...>...>>>.......<<<<<<<....>>>.
>>>>....>>...>>>>>>>>>>....<<<<<<<..<<<<<..<<<<<<<
.................>>>>>>><<<<<.....<<...<<<<<<<<<<]
]].>>>>>..>>>>>...>>...>>>>>.<<<<<...<<<<<........
...>>>>>...>>>>>>>>>>......>>>>>>>.<<..>><<<<<<<<<
<<<.......>>>>>....<<<<<<<<<<<<....<<<<<..<<<<....
>>>>..>>>>>...>>>>.>>>>>.>>>...>>>>>>>...

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8hl5 Cryo-EM Structures and Translocation Mechanism of Crenarchaeota Ribosome
• Resolution: 5.72 Å
• Binding residue (original residue number in PDB): V33 K35 D36 R39 R40 E45 K48 S49 Q51 K53 G54 R55 D56 A59 R62 T63 S64 I70 N71 G73 A75 R76 V77 P78 R79 P90 N91 V93 G94 R96 L97 F99 E104 K105 R106 E109 E110 N112 L113 K114 E115 K116 L118 F132 R136 K158 A159 R177 K182 R185 K188 K190 M191 R192 R194 R195 Y196 Q197 A199 K200 H209 E215 N219 S227 N229 L230 G239 H241
• Binding residue (residue number reindexed from 1): V25 K27 D28 R31 R32 E37 K40 S41 Q43 K45 G46 R47 D48 A51 R54 T55 S56 I62 N63 G65 A67 R68 V69 P70 R71 P82 N83 V85 G86 R88 L89 F91 E96 K97 R98 E101 E102 N104 L105 K106 E107 K108 L110 F124 R128 K150 A151 R169 K174 R177 K180 K182 M183 R184 R186 R187 Y188 Q189 A191 K192 H201 E207 N211 S219 N221 L222 G231 H233

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:8hl5, PDBe:8hl5, PDBj:8hl5
• PDBsum: 8hl5
• PubMed: 37604686
• UniProt: Q4JB41|RL4_SULAC Large ribosomal subunit protein uL4 (Gene Name=rpl4)