Structure of PDB 8hl2 Chain AL3P Binding Site BS01

Receptor Information

>8hl2 Chain AL3P (length=339) Species: 330779 (Sulfolobus acidocaldarius DSM 639)

RKLSSPRRGSAGLRPRKRADEILPTPKNWPLVNLKEPKLLGFIGYKAGMT
HVYMIDDKPTSPNYGKEVYTPVTIVESPPILGLALRAYHIDSKGELSVLV
DYWANFEEGSLKYLKRKITSLKVDSSKMKEKLDLIQKNLNNITYMRLLVS
TQPWLVPSLGKKRPEIVEIQIGGGSIQDQLNYGLSLLGKQIPVRDVFREG
QLTDIIGVTKGKGFQGVIKRYSVVEFPRWHKHRKGSRKIGARGPSISTPS
YVPQPGQLGFHRRTEYNKRIIKIGDNVNEINPAGGIVNYGLVKNTYLVIE
GSVLGSRKRPLFLRYPIRPSWSPESAPKITYVNLASQQG

Ligand information

>8hl2 Chain A23S (length=2996)

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
cuacugagauccucugguaggggggcgcugugaugggguagaaggugggu
cgugagauccacuggacccgucacaggugcagaucccggcgguaguaaca
gcgaaggggggugagaaucccccucgccggaagggcaaggguuucccggc
aacguucgucagccgggaguuagcguccuaagguagggccuaauagguac
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: 8hl2 Cryo-EM Structures and Translocation Mechanism of Crenarchaeota Ribosome
• Resolution: 4.1 Å
• Binding residue (original residue number in PDB): R4 K5 L6 S7 R10 R11 G12 S13 G15 R17 P18 R19 K20 R21 N31 M52 T53 H54 T63 P65 P74 R89 Y91 L99 S100 V101 D104 W106 R119 I121 S123 L124 K125 S128 R149 K164 K165 R166 E171 K213 G214 G216 F217 Q218 G219 K222 R223 V227 E228 F229 P230 R231 W232 H233 K234 R236 G238 R240 G243 A244 R245 P247 S248 I249 S250 P252 Y254 V255 Q257 P258 F263 R265 R266 T267 E268 Y269 K271 G287 V290 N291 G293 S305 V306 K311 R312 R321 Q341
• Binding residue (residue number reindexed from 1): R1 K2 L3 S4 R7 R8 G9 S10 G12 R14 P15 R16 K17 R18 N28 M49 T50 H51 T60 P62 P71 R86 Y88 L96 S97 V98 D101 W103 R116 I118 S120 L121 K122 S125 R146 K161 K162 R163 E168 K210 G211 G213 F214 Q215 G216 K219 R220 V224 E225 F226 P227 R228 W229 H230 K231 R233 G235 R237 G240 A241 R242 P244 S245 I246 S247 P249 Y251 V252 Q254 P255 F260 R262 R263 T264 E265 Y266 K268 G284 V287 N288 G290 S302 V303 K308 R309 R318 Q338

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:8hl2, PDBe:8hl2, PDBj:8hl2
• PDBsum: 8hl2
• PubMed: 37604686
• UniProt: Q4JB40|RL3_SULAC Large ribosomal subunit protein uL3 (Gene Name=rpl3)