Structure of PDB 7zw0 Chain sA Binding Site BS01

Receptor Information

>7zw0 Chain sA (length=222) Species: 580240 (Saccharomyces cerevisiae W303)

LISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRAT
RTQDVLGENGRRINELTLLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAE
SMKFKLLNGLAIRRAAYGVVRYVMESGAKGCEVVVSGKLRAARAKAMKFA
DGFLIHSGQPVNDFIDTATRHVLMRQGVLGIKVKIMRDPAKSRTGPKALP
DAVTIIEPKEEEPILAPSVKDY

Ligand information

>7zw0 Chain 2 (length=1765)

uaucugguugauccugccaguagucauaugcuugucucaaagauuaagcc
augcaugucuaaguauaagcaauuuauacagugaaacugcgaauggcuca
uuaaaucaguuaucguuuauuugauaguuccuuuacuacaugguauaacu
gugguaauucuagagcuaauacaugcuuaaaaucucgacccuuuggaaga
gauguauuuauuagauaaaaaaucaaugucuucggacucuuugaugauuc
auaauaacuuuucgaaucgcauggccuugugcuggcgaugguucauucaa
auuucugcccuaucaacuuucgaugguaggauaguggccuaccaugguuu
caacggguaacggggaauaaggguucgauuccggagagggagccugagaa
acggcuaccacauccaaggaaggcagcaggcgcgcaaauuacccaauccu
aauucagggagguagugacaauaaauaacgauacagggccggucuuguaa
uuggaaugaguacaauguaaauaccuuaacgaggaacaauuggagggcaa
gucuggugccagcagccgcgguaauuccagcuccaauagcguauauuaaa
guuguugcaguuaaaaagcucguaguugaacuuugggcccgguuggccgg
ucggauuuccaacggggccuuuccuucuggcuaaccuugagcuuggcgaa
ccaggacuuuuacuuugaaaaaauuagaguguucaaagcaggcguauugc
ucgaauauauuagcauggaauaauagaauaggacguuugguucuauuuug
uugguuucuaggaccaucguaaugauuaauagggacggucgggggcauca
guauucaauugucagaggugaaauucuuggauuuauugaagacuaacuac
ugcgaaagcauuugccaaggacguuuucauuaaucaagaacgaaaguuag
gggaucgaagaugaucagauaccgucguagucuuaaccauaaacuaugcc
gacuagggaucgggugguguuuuuuuaaugacccacucggcaccuuacga
gaaaucaaagucuuuggguucuggggggaguauggucgcaaggcugaaac
uuaaaggaauugacggaagggcaccaccaggaguggagccugcggcuuaa
uuugacucaacacggggaaacucaccagguccagacacaauaaggauuga
cagauugagagcucuuucuugauuuugugggugguggugcauggccguuc
uuaguugguggagugauuugucugcuuaauugcgauaacgaacgagaccu
uaaccuacuaaauaguggugcuagcauuugcugguuauccacuucuuaga
gggacuaucgguuucaagccgauggaaguuugaggcaauaacaggucugu
gaugcccuuagacguucugggccgcacgcgcgcuacacugacggagccag
cgagucuaaccuuggccgagaggucuugguaaucuugugaaacuccgucg
ugcuggggauagagcauuguaauuauugcucuucaacgaggaauuccuag
uaagcgcaagucaucagcuugcguugauuacgucccugcccuuuguacac
accgcccgucgcuaguaccgauugaauggcuuagugaggccucaggaucu
gcuuagagaagggggcaacuccaucucagagcggagaauuuggacaaacu
uggucauuuagaggaacuaaaagucguaacaagguuuccguaggugaacc
ugcggaaggaucauu

...<<<<<.{.[[[[>>>>><<<<.<<<<<<...<.<...<......<<<
.<<<..<<....<<....<<..........>>...>>.>>......<<..
......<<<..<<..<<....<<<..................<<....<<
.<<<.....>>>.>>.....>>.........<<<<<..<<....>>..>>
>>><...<<<<<<......(((((((.<<<....>>>....<........
>>>>>>>.....>...<<<<..<<<.....>>>.>>>>....>>>...>>
>>..>>>.<<<....<<<....<<<<<<<<.......>>>>>>>>>>>..
....>>>...<<<.<<<<....>>>>....>>>.>>.<<.<<<.......
...>>>.>>.<.<<....>>.>...>>>>>>.........<<<....<<<
.....>>>..>>>..>....>.>.....<<<<<<<<<.<..>.>>>>>>.
>>>......<<..<...........>..>>.........<<<<<((....
<.<<<<.....<<..))>>.......>>>>>>>>>>..>>>>>>>>>>..
.......<<<[[.....<.<<...<<<.<<....<<<<<<.<<<<.....
.........>>>>.>>>>>>....<<<<<<....................
>>>>>>...<<<<<.<<.......<<...<.......>..<<<.....>>
>....>>......>>.>>..>>>.........<<<..<<<<<<<<.....
))))))).>>>>>>>>.>>>.....>>....<<<<<<.<<...<<<<..<
<..<<<<<<.<...<<<......>>>......>.>>>>>>..>>......
.<<....>>...>>>>...>>>>>.>>>...>>>...>>.>....<<<<<
<<...<...<<<<.<.....>.>>>>...>>>>>>>>..........<<<
.<<.<<<..<<<<<<<<.<<<........>>>>>>>>>>>..>>>...<<
..]]>>...>>.....>>>.>>>.<<<......<<<<....>>>>....>
>>..]]]].}<<<<<.<<<<<<<..<<.<<<<<<..<<<.<<<<<<....
..<<........>>..........<<<<<.<....<<<<<........<<
.<<<........>>>.>>......>>>>>...<<.<<<..<<.<<<<<<.
...<<<.<<<<<....>>>...<<<......>>>...>>.>>>....<<<
<<.<<..<<<<..<<<<<.<<<<<<....>>>>>>...>>>>>..>>>>.
>>....<<<<<<.....>>>>>>.......>>>>>....>>>.>>>....
.>>>>>>>.....>.>>>>>...>>.>>>>.>>>.....<<<<<<<....
..<<.....<<..<<<<....>>>>..>>....>>.......>>>>>>>.
..........<<<<<<..........>>>>>>..........>>>>>>..
..<<<<<<<<.......>>>>>>>>......>>...>>>>>>>>>>.>>.
...<..<<.<..<<<<.<<....<<<<<<<<.<<<..<.<<..<...<<<
<<<<.<<<<.<<<<....>>>>.>>>>.>>>>>>>...>..>>.>..>>>
.>>>>>>>>...>>.>>>>...>.>>...>.....<<<<<<<<<<..>>>
>>>>>>>........

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7zw0 Sensing of individual stalled 80S ribosomes by Fap1 for nonfunctional rRNA turnover.
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): L4 I5 K7 K8 R9 R27 S139 K141 A145 R146 A147 K151 F156 L157 I158 H159 S160 G161 Q162 H174 L176 R178 V181 K185 P203 D204
• Binding residue (residue number reindexed from 1): L1 I2 K4 K5 R6 R24 S136 K138 A142 R143 A144 K148 F153 L154 I155 H156 S157 G158 Q159 H171 L173 R175 V178 K182 P200 D201

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0003906 DNA-(apurinic or apyrimidinic site) endonuclease activity
• GO:0005515 protein binding

Biological Process

• GO:0000054 ribosomal subunit export from nucleus
• GO:0000056 ribosomal small subunit export from nucleus
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0070651 nonfunctional rRNA decay
• GO:1990145 maintenance of translational fidelity

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015935 small ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0030686 90S preribosome
• GO:0030688 preribosome, small subunit precursor
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7zw0, PDBe:7zw0, PDBj:7zw0
• PDBsum: 7zw0
• PubMed: 36113412
• UniProt: P05750|RS3_YEAST Small ribosomal subunit protein uS3 (Gene Name=RPS3)