Structure of PDB 8cmj Chain j Binding Site BS01

Receptor Information
>8cmj Chain j (length=219) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKLNISYPVNGSQKTFEIDDEHRIRVFFDKRIGQEVDGEAVGDEFKGYVF
KISGGNDKQGFPMKQGVLLPTRIKLLLTKNVSCYRPRRDGERKRKSVRGA
IVGPDLAVLALVIVKKGEQELEGLTDTTVPKRLGPKRANNIRKFFGLSKE
DDVRDFVIRREVTKGEKTYTKAPKIQRLVTPQRLQRKRHQRALKVRNAQA
QREAAAEYAQLLAKRLSER
Ligand information
>8cmj Chain c (length=1608) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
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
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8cmj Cryo-EM analysis of eukaryotic ribosome translocation intermediates
Resolution3.79 Å
Binding residue
(original residue number in PDB)		K2 N4 Q13 T15 R31 S53 G54 N56 Q59 G60 Q65 G66 K74 L76 C83 Y84 R85 R87 R88 D89 E91 R92 R94 K95 S96 A110 R132 L133 K136 R137 N139 N140 K143 K149 D152 R154 R160 K167 A172 P173 K174 I175 Q176 R177 L178 V179 R183 L184 Q185 R186 K187 R188 H189 Q190 R191 K194 V195 N197 Q199 Q201 R202
Binding residue
(residue number reindexed from 1)		K2 N4 Q13 T15 R31 S53 G54 N56 Q59 G60 Q65 G66 K74 L76 C83 Y84 R85 R87 R88 D89 E91 R92 R94 K95 S96 A110 R132 L133 K136 R137 N139 N140 K143 K149 D152 R154 R160 K167 A172 P173 K174 I175 Q176 R177 L178 V179 R183 L184 Q185 R186 K187 R188 H189 Q190 R191 K194 V195 N197 Q199 Q201 R202
Enzymatic activity
Enzyme Commision number ?
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8cmj, PDBe:8cmj, PDBj:8cmj
PDBsum8cmj
PubMed38030725
UniProtP0CX37|RS6A_YEAST Small ribosomal subunit protein eS6A (Gene Name=RPS6A)

[Back to BioLiP]