Structure of PDB 8hl4 Chain AL3P Binding Site BS01

Receptor Information

>8hl4 Chain AL3P (length=339) Species: 330779 (Sulfolobus acidocaldarius DSM 639)

RKLSSPRRGSAGLRPRKRADEILPTPKNWPLVNLKEPKLLGFIGYKAGMT
HVYMIDDKPTSPNYGKEVYTPVTIVESPPILGLALRAYHIDSKGELSVLV
DYWANFEEGSLKYLKRKITSLKVDSSKMKEKLDLIQKNLNNITYMRLLVS
TQPWLVPSLGKKRPEIVEIQIGGGSIQDQLNYGLSLLGKQIPVRDVFREG
QLTDIIGVTKGKGFQGVIKRYSVVEFPRWHKHRKGSRKIGARGPSISTPS
YVPQPGQLGFHRRTEYNKRIIKIGDNVNEINPAGGIVNYGLVKNTYLVIE
GSVLGSRKRPLFLRYPIRPSWSPESAPKITYVNLASQQG

Ligand information

>8hl4 Chain A23S (length=2995)

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
acuagagauccucugguaggggggcgcugugaugggguagaagguggguc
gugagauccacuggacccgucacaggugcagaucccggcgguaguaacag
cgaaggggggugagaaucccccucgccggaagggcaaggguuucccggca
acguucgucagccgggaguuagccuccuaagguagggccuaauagguacc
uaccgaaagggaaagggguuaacauuccccugccucccggguaggugcgg
uaacgcaagccagacuccugacggauugggguagggagaguaggaccacc
guccuacccaagcacucaagcccuuggagagccguaacggugagaagagg
gcgaaggugugaugggccuuccguuaggaggguucuccugaucccuaguc
cccaugaaaagggagucuggaacgaucccgggagaccguaccuagaaccg
acacuggugcccgggugagaagcccaaggcgucugagggguaacccaggc
uagggaacucggcaaauuagccccguaacuucgggagaaggggugccuau
cgugguuuaacaaagccacgauaggucgcagugaccagagggaccugacu
guuuaauaaaaacauagguccccgcuagcccgaaaggguguguacggggg
cuaaauccuggccacuggugguugaaauccggguucaaccgggcgaagcc
ccaccgaaggccggggguaacucugacccucuuaagguagccaaaugccu
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: 8hl4 Cryo-EM Structures and Translocation Mechanism of Crenarchaeota Ribosome
• Resolution: 4.62 Å
• Binding residue (original residue number in PDB): R4 K5 S7 P9 R10 R11 S13 G15 R17 P18 K20 R21 K30 N31 M52 T53 H54 T63 P65 P74 R89 Y91 L99 S100 V101 W106 K115 R119 I121 S123 L124 K125 K134 G163 K164 K165 R166 E171 K213 G214 K215 G216 F217 Q218 G219 V227 P230 R231 W232 H233 R236 K237 G238 R240 G243 A244 R245 P247 S248 I249 P252 Y254 P258 Q260 F263 R265 R266 T267 Y269 N270 K271 N291 G293 E303 G304 S305 V306 L307 R310 R312 R317 I320 R321 Q341 G342
• Binding residue (residue number reindexed from 1): R1 K2 S4 P6 R7 R8 S10 G12 R14 P15 K17 R18 K27 N28 M49 T50 H51 T60 P62 P71 R86 Y88 L96 S97 V98 W103 K112 R116 I118 S120 L121 K122 K131 G160 K161 K162 R163 E168 K210 G211 K212 G213 F214 Q215 G216 V224 P227 R228 W229 H230 R233 K234 G235 R237 G240 A241 R242 P244 S245 I246 P249 Y251 P255 Q257 F260 R262 R263 T264 Y266 N267 K268 N288 G290 E300 G301 S302 V303 L304 R307 R309 R314 I317 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:8hl4, PDBe:8hl4, PDBj:8hl4
• PDBsum: 8hl4
• PubMed: 37604686
• UniProt: Q4JB40|RL3_SULAC Large ribosomal subunit protein uL3 (Gene Name=rpl3)