Structure of PDB 6tb3 Chain AA

Receptor sequence

>6tb3AA (length=233) Species: 559292 (Saccharomyces cerevisiae S288C)

NPLTHSTPKNFGIGQAVQPKRNLSRYVKWPEYVRVQRQKKILSIRLKVPP
TIAQFQYTLDRNTAAETFKLFNKYRPETAAEKKERLTKEAAAVAEGKSKQ
DASPKPYAVKYGLNHVVALIENKKAKLVLIANDVDPIELVVFLPALCKKM
GVPYAIVKGKARLGTLVNQKTSAVAALTEVRAEDEAALAKLVSTIDANFA
DKYDEVKKHWGGGILGNKAQAKMDKRAKNSDSA

3D structure

• PDB: 6tb3 The Ccr4-Not complex monitors the translating ribosome for codon optimality.
• Chain: AA
• Resolution: 2.8 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	AA	T27 H28 S29 T30 P31 K32 N33 F34 Q38 Q41 P42 R44 L46 S47 R48 Y49 K51 P53 E54 Y55 R57 R60 L65 R68 L69 K70 E100 K105 R108 S126 P127 K128 P129 K133 Y134 G135 L136 N137 H138 A141 L142 N145 K147 V157 D158 L162 K183 A184 Q192 K193 S195 A196 G239 N240 K241 A242 K248	T4 H5 S6 T7 P8 K9 N10 F11 Q15 Q18 P19 R21 L23 S24 R25 Y26 K28 P30 E31 Y32 R34 R37 L42 R45 L46 K47 E77 K82 R85 S103 P104 K105 P106 K110 Y111 G112 L113 N114 H115 A118 L119 N122 K124 V134 D135 L139 K160 A161 Q169 K170 S172 A173 G216 N217 K218 A219 K225
BS02	rna	AA	Y55 Q59 R60 K63 R84 K181 R185	Y32 Q36 R37 K40 R61 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:6tb3, PDBe:6tb3, PDBj:6tb3
• PDBsum: 6tb3
• PubMed: 32299921
• UniProt: P17076|RL8A_YEAST Large ribosomal subunit protein eL8A (Gene Name=RPL8A)