Structure of PDB 8hku Chain AL2P Binding Site BS01

Receptor Information

>8hku Chain AL2P (length=234) Species: 330779 (Sulfolobus acidocaldarius DSM 639)

GKKLLQQRAGRGGINFRSPSWRRVGPARYPNIEGDHKGKIIDILHNPGVT
APVVKVKLDNGLQFYIPAVQGVAVGQEISIGKNATISNGNIVEVGQLPEG
TVICNVEKLKGDGGKFARAAGSYAVISGKAGNKVLIKLSSEKIVEVSQNA
RATVGIIAGGGFVEKPLLKAGNNYWKYRVRAVKWPVVRGVAMNAVSHPHG
GGLHQSVSRPSTVSRNAPPGRKVGHIASRRTGRR

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): G2 K3 K4 Q7 Q8 R9 G11 R12 I15 N16 R18 S19 S21 W22 R24 G26 R29 N32 H46 K109 K116 F117 A118 R119 A120 A121 L139 S140 S141 K143 V145 F163 K166 L168 L169 K170 A171 G172 Y175 W176 K177 K184 W185 P186 V187 V188 R189 V191 A192 M193 N194 V196 H200 G202 G203 L204 H205 S207 S209 R210 S212 T213 V214 S215 R216 N217 P219 P220 V224 G225 H226 I227 A228 S229 R230 R231 T232 G233 R234
• Binding residue (residue number reindexed from 1): G1 K2 K3 Q6 Q7 R8 G10 R11 I14 N15 R17 S18 S20 W21 R23 G25 R28 N31 H45 K108 K115 F116 A117 R118 A119 A120 L138 S139 S140 K142 V144 F162 K165 L167 L168 K169 A170 G171 Y174 W175 K176 K183 W184 P185 V186 V187 R188 V190 A191 M192 N193 V195 H199 G201 G202 L203 H204 S206 S208 R209 S211 T212 V213 S214 R215 N216 P218 P219 V223 G224 H225 I226 A227 S228 R229 R230 T231 G232 R233

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• 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:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8hku, PDBe:8hku, PDBj:8hku
• PDBsum: 8hku
• PubMed: 37604686
• UniProt: Q4JB43|RL2_SULAC Large ribosomal subunit protein uL2 (Gene Name=rpl2)