Structure of PDB 8agu Chain B

Receptor sequence

>8aguB (length=197) Species: 4932 (Saccharomyces cerevisiae)

VEPVVVIDGKGHLVGRLASVVAKQLLNGQKIVVVRAEELNISGEFFRNKL
KYHDFLRKATAFNKTRGPFHFRAPSRIFYKALRGMVSHKTARGKAALERL
KVFEGIPPPYDKKKRVVVPQALRVLRLKPGRKYTTLGKLSTSVGWKYEDV
VAKLEAKRKVSSAEYYAKKRAFTKKVASANATAAESDVAKQLAALGY

3D structure

• PDB: 8agu Molecular basis of eIF5A-dependent CAT tailing in eukaryotic ribosome-associated quality control.
• Chain: B
• Resolution: 2.7 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	rna	B	E4 P5 V6 K12 G17 R18 S21 K25 R37 S44 F48 R49 H55 R59 K60 A61 T62 F64 N65 K66 R68 P70 F71 H72 F73 R74 K82 A83 R85 G86 M87 S89 H90 K91 A93 R94 A97 R101 F105 I108 P110 D113 K114 K115 R117 Q122 V126 R128 L129 K130 R133 K134 K148 Y149 L156 K159 K161 S164 Y167 Y168 K171 R172	E2 P3 V4 K10 G15 R16 S19 K23 R35 S42 F46 R47 H53 R57 K58 A59 T60 F62 N63 K64 R66 P68 F69 H70 F71 R72 K80 A81 R83 G84 M85 S87 H88 K89 A91 R92 A95 R99 F103 I106 P108 D111 K112 K113 R115 Q120 V124 R126 L127 K128 R131 K132 K146 Y147 L154 K157 K159 S162 Y165 Y166 K169 R170

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0000470 maturation of LSU-rRNA
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0017148 negative regulation of translation

Cellular Component

• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8agu, PDBe:8agu, PDBj:8agu
• PDBsum: 8agu
• PubMed: 36804914
• UniProt: P26784|RL16A_YEAST Large ribosomal subunit protein uL13A (Gene Name=RPL16A)