Structure of PDB 8hl3 Chain AL3P Binding Site BS01

Receptor Information

>8hl3 Chain AL3P (length=339) Species: 330779 (Sulfolobus acidocaldarius DSM 639)

RKLSSPRRGSAGLRPRKRADEILPTPKNWPLVNLKEPKLLGFIGYKAGMT
HVYMIDDKPTSPNYGKEVYTPVTIVESPPILGLALRAYHIDSKGELSVLV
DYWANFEEGSLKYLKRKITSLKVDSSKMKEKLDLIQKNLNNITYMRLLVS
TQPWLVPSLGKKRPEIVEIQIGGGSIQDQLNYGLSLLGKQIPVRDVFREG
QLTDIIGVTKGKGFQGVIKRYSVVEFPRWHKHRKGSRKIGARGPSISTPS
YVPQPGQLGFHRRTEYNKRIIKIGDNVNEINPAGGIVNYGLVKNTYLVIE
GSVLGSRKRPLFLRYPIRPSWSPESAPKITYVNLASQQG

Ligand information

>8hl3 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: 8hl3 Cryo-EM Structures and Translocation Mechanism of Crenarchaeota Ribosome
• Resolution: 4.8 Å
• Binding residue (original residue number in PDB): R4 K5 S7 R10 R11 S13 A14 G15 R17 P18 R19 K20 R21 I25 T28 N31 M52 T53 H54 T63 P65 P74 R89 Y91 L99 S100 V101 L102 D104 R119 K120 I121 S123 L124 K125 S128 K164 K165 R166 I169 E171 T212 K213 G214 K215 G216 F217 Q218 G219 K222 V227 E228 F229 P230 R231 W232 R236 K237 G238 S239 R240 G243 A244 R245 S248 I249 S250 R265 R266 T267 Y269 N270 G287 N291 G293 S305 V306 R312 R321 S339 Q341 G342
• Binding residue (residue number reindexed from 1): R1 K2 S4 R7 R8 S10 A11 G12 R14 P15 R16 K17 R18 I22 T25 N28 M49 T50 H51 T60 P62 P71 R86 Y88 L96 S97 V98 L99 D101 R116 K117 I118 S120 L121 K122 S125 K161 K162 R163 I166 E168 T209 K210 G211 K212 G213 F214 Q215 G216 K219 V224 E225 F226 P227 R228 W229 R233 K234 G235 S236 R237 G240 A241 R242 S245 I246 S247 R262 R263 T264 Y266 N267 G284 N288 G290 S302 V303 R309 R318 S336 Q338 G339

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:8hl3, PDBe:8hl3, PDBj:8hl3
• PDBsum: 8hl3
• PubMed: 37604686
• UniProt: Q4JB40|RL3_SULAC Large ribosomal subunit protein uL3 (Gene Name=rpl3)