Structure of PDB 8hky Chain AL3P Binding Site BS01

Receptor Information

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

RKLSSPRRGSAGLRPRKRADEILPTPKNWPLVNLKEPKLLGFIGYKAGMT
HVYMIDDKPTSPNYGKEVYTPVTIVESPPILGLALRAYHIDSKGELSVLV
DYWANFEEGSLKYLKRKITSLKVDSSKMKEKLDLIQKNLNNITYMRLLVS
TQPWLVPSLGKKRPEIVEIQIGGGSIQDQLNYGLSLLGKQIPVRDVFREG
QLTDIIGVTKGKGFQGVIKRYSVVEFPRWHKHRKGSRKIGARGPSISTPS
YVPQPGQLGFHRRTEYNKRIIKIGDNVNEINPAGGIVNYGLVKNTYLVIE
GSVLGSRKRPLFLRYPIRPSWSPESAPKITYVNLASQQG

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): R4 K5 R10 R11 S13 A14 G15 R17 P18 R19 K20 R21 D23 K30 N31 M52 T63 P65 R89 Y91 L99 S100 D104 W106 R119 K120 I121 S123 L124 K125 G163 K164 K165 R166 I169 V170 E171 T212 I221 K222 V226 V227 F229 P230 R231 W232 K234 R236 K237 G238 R240 I242 G243 A244 R245 G246 P247 S248 I249 T251 P252 S253 Y254 Q257 P258 Q260 F263 R265 R266 T267 Y269 N270 K271 I289 V290 N291 G293 S305 V306 L307 S309 R310 R312 R321 Q341 G342
• Binding residue (residue number reindexed from 1): R1 K2 R7 R8 S10 A11 G12 R14 P15 R16 K17 R18 D20 K27 N28 M49 T60 P62 R86 Y88 L96 S97 D101 W103 R116 K117 I118 S120 L121 K122 G160 K161 K162 R163 I166 V167 E168 T209 I218 K219 V223 V224 F226 P227 R228 W229 K231 R233 K234 G235 R237 I239 G240 A241 R242 G243 P244 S245 I246 T248 P249 S250 Y251 Q254 P255 Q257 F260 R262 R263 T264 Y266 N267 K268 I286 V287 N288 G290 S302 V303 L304 S306 R307 R309 R318 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:8hky, PDBe:8hky, PDBj:8hky
• PDBsum: 8hky
• PubMed: 37604686
• UniProt: Q4JB40|RL3_SULAC Large ribosomal subunit protein uL3 (Gene Name=rpl3)