Structure of PDB 8ccs Chain q Binding Site BS02

Receptor Information

>8ccs Chain q (length=127) Species: 4932 (Saccharomyces cerevisiae)

SQVFGVARIYASFNDTFVHVTDLSGKETIARVTGGMKVKADRDESSPYAA
MLAAQDVAAKCKEVGITAVHVKIRATGGTRTKTPGPGGQAALRALARSGL
RIGRIEDVTPVPSDSTRKKGGRRGRRL

Ligand information

>8ccs Chain c (length=1604)

uaucugguugauccugccaguagucauaugcuugucucaaagauuaagcc
augcaugucuaaguauaagcaauacagugaaacugcgaauggcucauuaa
aucaguuaucguuuauuugauaguucccuacaugguauaacugugguaau
ucuagagcuaauacaugcuuaaaaucucagauguauuuauuagauugaug
auucauaauaacuuuucgaaucgcauggccuugugcuggcgaugguucau
ucaaauuucugcccuaucaacuuucgaugguaggauaguggccuaccaug
guuucaacggguaacggggaauaaggguucgauuccggagagggagccug
agaaacggcuaccacauccaaggaaggcagcaggcgcgcaaauuacccaa
uccuaauucagggagguagugacaauaaauaacgauacauguaauuggaa
ugaguacaauguaaauaccuuaacgaggaacaauuggagggcaagucugg
ugccagcagccgcgguaauuccagcuccaauagcguauauuaaaguuguu
gcaguuaaaaagcucguaguugaacuuugggcccgguugcaacggggccu
uuccuuuacuuugaaaaaauuagaguguucaaagcaggcguauugcucga
auauauuagcauggaauaauagaauaggacguuuaucguaaugauuaaua
gggacggucgggggcaucaguauucaauugucagaggugaaauucuugga
uuuauugaagacuaacuacugcgaaagcauuugccaaggacguuuucauu
aaucaagaacgaaaguuaggggaucgaagaugaucagauaccgucguagu
cuuaaccauaaacuaugccgacuagggaucgggugguguuuuuuuaauga
cccacucggcaccuuacgagaaaucaaagucuuuggguucuggggggagu
auggucgcaaggcugaaacuuaaaggaauugacggaagggcaccaccagg
aguggagccugcggcuuaauuugacucaacacggggaaacucaccagguc
cagacacaauaaggauugacagauugagagcucuuucuugauuuuguggg
ugguggugcauggccguucuuaguugguggagugauuugucugcuuaauu
gcgauaacgaacgagaccuuaaccuacuaaauaguggugcuagcauuugc
ugguuauccacuucuuagagggacuaucgguuucaagccgauggaaguuu
gaggcaauaacaggucugugaugcccuuagacguucugggccgcacgcgc
gcuacacugacggagccagcgagucuaaccuuggccgagaggucuuggua
aucuugugaaacuccgucgugcuggggauagagcauuguaauuauugcuc
uucaacgaggaauuccuaguaagcgcaagucaucagcuugcguugauuac
gucccugcccuuuguacacaccgcccgucgcuaguaccgauugaauggcu
uagugaggccucaggaucugcggagaauuuggacaaacuuggucauuuag
aggaacuaaaagucguaacaagguuuccguaggugaaccugcggaaggau
cauu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8ccs Cryo-EM analysis of eukaryotic ribosome translocation intermediates
• Resolution: 1.97 Å
• Binding residue (original residue number in PDB): R18 N24 D25 F27 H29 G35 T38 R41 T43 G45 M46 K49 D51 R52 E54 R84 G88 R90 P120 V121 P122 S123 D124 T126 R127 K129 G130 G131 R132 R133 R135 R136 L137
• Binding residue (residue number reindexed from 1): R8 N14 D15 F17 H19 G25 T28 R31 T33 G35 M36 K39 D41 R42 E44 R74 G78 R80 P110 V111 P112 S113 D114 T116 R117 K119 G120 G121 R122 R123 R125 R126 L127

Gene Ontology

Molecular Function

• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0000028 ribosomal small subunit assembly
• GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0002181 cytoplasmic translation
• 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:8ccs, PDBe:8ccs, PDBj:8ccs
• PDBsum: 8ccs
• PubMed: 38030725
• UniProt: P06367|RS14A_YEAST Small ribosomal subunit protein uS11A (Gene Name=RPS14A)