Structure of PDB 5jut Chain L

Receptor sequence

>5jutL (length=233) Species: 4932 (Saccharomyces cerevisiae)

NPLTHSTPKNFGIGQAVQPKRNLSRYVKWPEYVRVQRQKKILSIRLKVPP
TIAQFQYTLDRNTAAETFKLFNKYRPETAAEKKERLTKEAAAVAEGKSKQ
DASPKPYAVKYGLNHVVALIENKKAKLVLIANDVDPIELVVFLPALCKKM
GVPYAIVKGKARLGTLVNQKTSAVAALTEVRAEDEAALAKLVSTIDANFA
DKYDEVKKHWGGGILGNKAQAKMDKRAKNSDSA

3D structure

• PDB: 5jut Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome.
• Chain: L
• Resolution: 4.0 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	L	N24 S29 K32 N33 F34 G35 I36 G37 Q41 P42 R44 S47 R48 Y49 K51 P53 E54 Y55 R60 R68 L69 E100 K105 R108 D124 S126 K128 P129 Y134 G135 N137 H138 A141 N145 V157 K183 A184 Q192 K193 T194 S195 L238 G239 K241 A242 A244 K245 K248 R249	N1 S6 K9 N10 F11 G12 I13 G14 Q18 P19 R21 S24 R25 Y26 K28 P30 E31 Y32 R37 R45 L46 E77 K82 R85 D101 S103 K105 P106 Y111 G112 N114 H115 A118 N122 V134 K160 A161 Q169 K170 T171 S172 L215 G216 K218 A219 A221 K222 K225 R226
BS02	rna	L	Y55 V56 Q59 R60 K181 R185	Y32 V33 Q36 R37 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:5jut, PDBe:5jut, PDBj:5jut
• PDBsum: 5jut
• PubMed: 27159452
• UniProt: P17076|RL8A_YEAST Large ribosomal subunit protein eL8A (Gene Name=RPL8A)