Structure of PDB 8cdr Chain j Binding Site BS01

Receptor Information

>8cdr Chain j (length=219) Species: 4932 (Saccharomyces cerevisiae)

MKLNISYPVNGSQKTFEIDDEHRIRVFFDKRIGQEVDGEAVGDEFKGYVF
KISGGNDKQGFPMKQGVLLPTRIKLLLTKNVSCYRPRRDGERKRKSVRGA
IVGPDLAVLALVIVKKGEQELEGLTDTTVPKRLGPKRANNIRKFFGLSKE
DDVRDFVIRREVTKGEKTYTKAPKIQRLVTPQRLQRKRHQRALKVRNAQA
QREAAAEYAQLLAKRLSER

Ligand information

>8cdr Chain c (length=1608)

uaucugguugauccugccaguagucauaugcuugucucaaagauuaagcc
augcaugucuaaguauaagcaauacagugaaacugcgaauggcucauuaa
aucaguuaucguuuauuugauaguucccuacaugguauaacugugguaau
ucuagagcuaauacaugcuuaaaaucucagauguauuuauuagauugaug
auucauaauaacuuuucgaaucgcauggccuugugcuggcgaugguucau
ucaaauuucugcccuaucaacuuucgaugguaggauaguggccuaccaug
guuucaacggguaacggggaauaaggguucgauuccggagagggagccug
agaaacggcuaccacauccaaggaaggcagcaggcgcgcaaauuacccaa
uccuaauucagggagguagugacaauaaauaacgauacauguaauuggaa
ugaguacaauguaaauaccuuaacgaggaacaauuggagggcaagucugg
ugccagcagccgcgguaauuccagcuccaauagcguauauuaaaguuguu
gcaguuaaaaagcucguaguugaacuuugggcccgguugcaacggggccu
uucuuuuacuuugaaaaaauuagaguguucaaagcaggcguauugcucga
auauauuagcauggaauaauagaauaggacguuuaucguaaugauuaaua
gggacggucgggggcaucaguauucaauugucagaggugaaauucuugga
uuuauugaagacuaacuacugcgaaagcauuugccaaggacguuuucauu
aaucaagaacgaaaguuaggggaucgaagaugaucagauaccgucguagu
cuuaaccauaaacuaugccgacuagggaucgggugguguuuuuuuaauga
cccacucggcaccuuacgagaaaucaaagucuuuggguucuggggggagu
auggucgcaaggcugaaacuuaaaggaauugacggaagggcaccaccagg
aguggagccugcggcuuaauuugacucaacacggggaaacucaccagguc
cagacacaauaaggauugacagauugagagcucuuucuugauuuuguggg
ugguggugcauggccguucuuaguugguggagugauuugucugcuuaauu
gcgauaacgaacgagaccuuaaccuacuaaauaguggugcuagcauuugc
ugguuauccacuucuuagagggacuaucgguuucaagccgauggaaguuu
gaggcaauaacaggucugugaugcccuuagacguucugggccgcacgcgc
gcuacacugacggagccagcgagucuaaccuuggccgagaggucuuggua
aucuugugaaacuccgucgugcuggggauagagcauuguaauuauugcuc
uucaacgaggaauuccuaguaagcgcaagucaucagcuugcguugauuac
gucccugcccuuuguacacaccgcccgucgcuaguaccgauugaauggcu
uagugaggccucaggaucugcuagcggagaauuuggacaaacuuggucau
uuagaggaacuaaaagucguaacaagguuuccguaggugaaccugcggaa
ggaucauu

...<<<<<.[.((((>>>>><<<<.<<<<<<...<.<...<......<<<
.<<<..<<....<<....<<......>>...>>.>>......<<......
..<<<..<<..<<....<<<............<<......<<.<<.....
..>>.>>......>>........<<<<.>>>><...<<<<<<........
.....>>>>>>.....>...<<<<.<<<<.....>>>>>>>>....>>>.
..>>>>..>>>.<<<....<<<....<<<<<<<<.......>>>>>>>>>
>>......>>>...<<<.<<<<....>>>>....>>>.>>.<<.<<<...
.......>>>.>>.<.<<....>>.>...>>>>>>.........<<<...
.<<<.....>>>..>>>..>....>.>.....<<<<<<..>>>.>>>...
...<<.................>>.........<<<<<((....<.<<<<
.....<<..))>>.......>>>>>>>>>>..>>>>>>>>>>........
.<<<((.....<.<<...<<<.<<....<<<<<<.<<<..>>>.>>>>>>
.....<<<<<.<<.......<<...<.......>..<<<.....>>>...
.>>......>>.>>..>>>.........<<<.<.>.>>>.....>>....
<<<<<<.<<...<<<<..<<..<<<<<<.<...<<<......>>>.....
.>.>>>>>>..>>.......<<....>>...>>>>...>>>>>.>>>...
>>>...>>.>....<<<<<<<...<...<<<<.<.....>.>>>>...>>
>>>>>>..........<<<.<<.<<<..<<<<<<<<.<<<<.....>.>>
>>>>>>>>>..>>>...<<..))>>...>>.....>>>.>>>.<<<....
..<<<<....>>>>....>>>..)))).]<<<<<.<<<<<<<..<<.<<<
<<<..<<<.<<<<<.......<<........>>..........<<<<<.<
....<<<<<........<<.<<<........>>>.>>......>>>>>..
.<<.<<<..<<<<<<<<<....<<<.<<<<<....>>>...<<<......
>>>...>>.>>>....<<<<<.<<..<<<<..<<<<<.<..<<<....>>
>..>...>>>>>..>>>>.>>....<<<<<<.....>>>>>>.......>
>>>>....>>>.>>>...>.>>>>>>>.....>.>>>>>....>.>>>>.
>>>.....<<<<<<<......<<.....<<..<<<<....>>>>..>>..
..>>.......>>>>>>>......<....<<<<<<..........>>>>>
>....>.....>>>>>>....<<<<<<<<.......>>>>>>>>......
>>...>>>>>>>>>>.>>....<..<<.<..<<<<.<<....<<<<<<<<
.<<<..<.<<..<...<<<<<..>>>>>...>..>>.>..>>>.>>>>>>
>>...>>.>>>>...>.>>...>.....<<<<<<<<<<..>>>>>>>>>>
........

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8cdr mRNA reading frame maintenance during eukaryotic ribosome translocation
• Resolution: 2.04 Å
• Binding residue (original residue number in PDB): K2 N4 S6 P8 Q13 T15 S53 N56 Q59 G60 F61 Q65 G66 V67 R72 K74 L75 L76 S82 C83 Y84 R85 R87 R88 G90 R92 R94 K95 S96 V108 K131 R132 L133 G134 P135 K136 R137 N139 N140 R159 R160 K171 A172 P173 K174 I175 Q176 R177 L178 V179 R183 L184 Q185 R186 K187 R188 Q190 R191 A192 K194 V195 R196 A198 Q201 R202 L216
• Binding residue (residue number reindexed from 1): K2 N4 S6 P8 Q13 T15 S53 N56 Q59 G60 F61 Q65 G66 V67 R72 K74 L75 L76 S82 C83 Y84 R85 R87 R88 G90 R92 R94 K95 S96 V108 K131 R132 L133 G134 P135 K136 R137 N139 N140 R159 R160 K171 A172 P173 K174 I175 Q176 R177 L178 V179 R183 L184 Q185 R186 K187 R188 Q190 R191 A192 K194 V195 R196 A198 Q201 R202 L216

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0042254 ribosome biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0030686 90S preribosome
• GO:0032040 small-subunit processome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8cdr, PDBe:8cdr, PDBj:8cdr
• PDBsum: 8cdr
• PubMed: 38030725
• UniProt: P0CX37|RS6A_YEAST Small ribosomal subunit protein eS6A (Gene Name=RPS6A)