Structure of PDB 8cmj Chain p Binding Site BS02

Receptor Information

>8cmj Chain p (length=150) Species: 4932 (Saccharomyces cerevisiae)

GRMHSAGKGISSSAIPYSRNAPAWFKLSSESVIEQIVKYARKGLTPSQIG
VLLRDAHGVTQARVITGNKIMRILKSNGLAPEIPEDLYYLIKKAVSVRKH
LERNRKDKDAKFRLILIESRIHRLARYYRTVAVLPPNWKYESATASALVN

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): G2 R3 M4 H5 K9 G10 I11 S12 S14 I16 P17 S48 G51 V52 R55 T61 Q62 R64 K70 M72 R73 K76 Y90 H101 R104 K107 D108 K109 D110 K112 F113 R114 R121 R124 R127 Y128
• Binding residue (residue number reindexed from 1): G1 R2 M3 H4 K8 G9 I10 S11 S13 I15 P16 S47 G50 V51 R54 T60 Q61 R63 K69 M71 R72 K75 Y89 H100 R103 K106 D107 K108 D109 K111 F112 R113 R120 R123 R126 Y127

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0070181 small ribosomal subunit rRNA binding

Biological Process

• GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005730 nucleolus
• 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: P05756|RS13_YEAST Small ribosomal subunit protein uS15 (Gene Name=RPS13)