Structure of PDB 8cmj Chain s Binding Site BS01

Receptor Information

>8cmj Chain s (length=136) Species: 4932 (Saccharomyces cerevisiae)

VQTFGKKKSATAVAHVKAGKGLIKVNGSPITLVEPEILRFKVYEPLLLVG
LDKFSNIDIRVRVTGGGHVSQVYAIRQAIAKGLVAYHQKYVDEQSKNELK
KAFTSYDRTLLIADSRRPEPKKFGGKGARSRFQKSY

Ligand information

>8cmj 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: 8cmj Cryo-EM analysis of eukaryotic ribosome translocation intermediates
• Resolution: 3.79 Å
• Binding residue (original residue number in PDB): Q8 T9 F10 K12 H21 K30 P41 E42 G71 G72 G73 H74 V75 Q77 S121 R122 P124 E125 K128 F129 G133 A134 R135 S136 F138 Q139 K140 S141 Y142
• Binding residue (residue number reindexed from 1): Q2 T3 F4 K6 H15 K24 P35 E36 G65 G66 G67 H68 V69 Q71 S115 R116 P118 E119 K122 F123 G127 A128 R129 S130 F132 Q133 K134 S135 Y136

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• 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:0006412 translation
• GO:0006413 translational initiation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0030686 90S preribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8cmj, PDBe:8cmj, PDBj:8cmj
• PDBsum: 8cmj
• PubMed: 38030725
• UniProt: P0CX51|RS16A_YEAST Small ribosomal subunit protein uS9A (Gene Name=RPS16A)