Structure of PDB 7uck Chain DD Binding Site BS01

Receptor Information

>7uck Chain DD (length=228) Species: 9986 (Oryctolagus cuniculus)

MAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIII
LATRTQNVLGEKGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIA
QAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVVVSGKLRGQRAKSM
KFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKVKIMLPWDPSGKIGP
KKPLPDHVSIVEPKDEILPTTPISEQKG

Ligand information

>7uck Chain 9 (length=1698)

uaccugguugauccugccaguagcauaugcuugucucaaagauuaagcca
ugcaugucuaaguacgcacggccgguacagugaaacugcgaauggcucau
uaaaucaguuaugguuccuuuggucgcucguacuuggauaacugugguaa
uucuagagcuaauacaugccgacgggcgcugacccccuucgcggggggga
ugcgugcauuuaucaguggugacucuagauaaccucgggccgaucgcacg
cccggcggcgacgacccauucgaacgucugcccuaucaacuuucgauggu
agucgccgugccuaccauggugaccacgggugacggggaaucaggguucg
auuccggagagggagccugagaaacggcuaccacauccaaggaaggcagc
aggcgcgcaaauuacccacucccgacccggggagguagugacgaaaaaua
acaauacaggacucuuucgaggcccuguaauuggaaugaguccacuuuaa
auccuuuaacgaggauccauuggagggcaagucuggugccagcagccgcg
guaauuccagcuccaauagcguauauuaaaguugcugcaguuaaaaagcu
cguaguuggaucuugggagcggccguccccugcucggcgccggcccgaag
cguuuacuuugaaaaaauuagaguguucaaagcaggccgccuggauaccg
cagcuaggaauaauggaauaggaccgcgguucuauuuuguugguuuucgg
aacugaggccaugauuaagagggacggccgggggcauucguauugcgccg
cuagaggugaaauucuuggaccggcgcaagacggaccagagcgaaagcau
uugccaagaauguuuucauuaaucaagaacgaaagucggagguucgaaga
cgaucagauaccgucguaguuccgaccauaaacgaugccgacuggcgaug
cggcggcguuauucccaugacccgccgggcagcuuccgggaaaccaaagu
cuuuggguuccggggggaguaugguugcaaagcugaaacuuaaaggaauu
gacggaagggcaccaccaggaguggagccugcggcuuaauuugacucaac
acgggaaaccucacccggcccggacacggacaggauugacagauugauag
cucuuucucgauuccgugggugguggugcauggccguucuuaguuggugg
agcgauuugucugguuaauuccgauaacgaacgagacucuggcaugcuaa
cuaguuacgcgaccccggucggcguaacuucuuagagggacaaguggcgu
ucagccacccgagauugagcaauaacaggucugugaugcccuuagauguc
cggggcugcacgcgcgcuacacugacuggcucagcgugugccuacccuac
gccggcaggcgcggguaacccguugaaccccauucgugauggggaucggg
gauugcaauuauuccccaugaacgaggaauucccaguaagugcgggucau
aagcuugcguugauuaagucccugcccuuuguacacaccgcccgucgcua
cuaccgauuggaugguuuagugaggcccucggaucggccccgccggggug
cccuggcggagcgcugagaagacggucgaacuugacuaucuagaggaagu
aaaagucguaacaagguuuccguaggugaaccugcggaaggaucauua

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7uck Direct epitranscriptomic regulation of mammalian translation initiation through N4-acetylcytidine.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): V3 Q4 I5 S6 K8 R9 R27 S139 K141 Q145 R146 A147 K151 M157 H159 S160 G161 D162 V172 H174 L176 Q179 V181 G183 D206
• Binding residue (residue number reindexed from 1): V3 Q4 I5 S6 K8 R9 R27 S139 K141 Q145 R146 A147 K151 M157 H159 S160 G161 D162 V172 H174 L176 Q179 V181 G183 D206

Enzymatic activity

• Enzyme Commision number: 4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0003906 DNA-(apurinic or apyrimidinic site) endonuclease activity
• GO:0016829 lyase activity
• GO:0140078 class I DNA-(apurinic or apyrimidinic site) endonuclease activity

Biological Process

• GO:0006281 DNA repair
• GO:0006412 translation
• GO:0006417 regulation of translation
• GO:0006915 apoptotic process
• GO:0031334 positive regulation of protein-containing complex assembly
• GO:0051092 positive regulation of NF-kappaB transcription factor activity
• GO:0051301 cell division
• GO:2001235 positive regulation of apoptotic signaling pathway

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005739 mitochondrion
• GO:0005743 mitochondrial inner membrane
• GO:0005819 spindle
• GO:0005840 ribosome
• GO:0005856 cytoskeleton
• GO:0015935 small ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0045202 synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7uck, PDBe:7uck, PDBj:7uck
• PDBsum: 7uck
• PubMed: 35679869
• UniProt: G1TNM3|RS3_RABIT Small ribosomal subunit protein uS3 (Gene Name=RPS3)