Structure of PDB 3j6x Chain L8

Receptor sequence

>3j6xL8 (length=233) Species: 580240 (Saccharomyces cerevisiae W303)

NPLTHSTPKNFGIGQAVQPKRNLSRYVKWPEYVRVQRQKKILSIRLKVPP
TIAQFQYTLDRNTAAETFKLFNKYRPETAAEKKERLTKEAAAVAEGKSKQ
DASPKPYAVKYGLNHVVALIENKKAKLVLIANDVDPIELVVFLPALCKKM
GVPYAIVKGKARLGTLVNQKTSAVAALTEVRAEDEAALAKLVSTIDANFA
DKYDEVKKHWGGGILGNKAQAKMDKRAKNSDSA

3D structure

• PDB: 3j6x Taura syndrome virus IRES initiates translation by binding its tRNA-mRNA-like structural element in the ribosomal decoding center.
• Chain: L8
• Resolution: 6.1 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	L8	S29 T30 P31 K32 F34 G35 I36 G37 Q38 K43 R44 L46 R48 Y49 V50 K51 E54 Y55 R68 K70 K105 R108 P127 K128 P129 Y134 G135 L136 H138 A141 L142 N145 V157 D158 P159 L162 Q192 K193 T194 S195 G239 N240 K241 A242 A244 K248 R249	S6 T7 P8 K9 F11 G12 I13 G14 Q15 K20 R21 L23 R25 Y26 V27 K28 E31 Y32 R45 K47 K82 R85 P104 K105 P106 Y111 G112 L113 H115 A118 L119 N122 V134 D135 P136 L139 Q169 K170 T171 S172 G216 N217 K218 A219 A221 K225 R226
BS02	rna	L8	R60 K63 K181 R185	R37 K40 K158 R162

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000470 maturation of LSU-rRNA
• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0042254 ribosome biogenesis

Cellular Component

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

External links

• PDB: RCSB:3j6x, PDBe:3j6x, PDBj:3j6x
• PDBsum: 3j6x
• PubMed: 24927574
• UniProt: P17076|RL8A_YEAST Large ribosomal subunit protein eL8A (Gene Name=RPL8A)