Structure of PDB 6tb3 Chain Y

Receptor sequence

>6tb3Y (length=150) Species: 559292 (Saccharomyces cerevisiae S288C)

GRMHSAGKGISSSAIPYSRNAPAWFKLSSESVIEQIVKYARKGLTPSQIG
VLLRDAHGVTQARVITGNKIMRILKSNGLAPEIPEDLYYLIKKAVSVRKH
LERNRKDKDAKFRLILIESRIHRLARYYRTVAVLPPNWKYESATASALVN

3D structure

• PDB: 6tb3 The Ccr4-Not complex monitors the translating ribosome for codon optimality.
• Chain: Y
• 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	Y	G2 R3 M4 H5 G8 K9 G10 I11 S12 S14 A15 I16 P17 S48 G51 R55 T61 R64 K70 M72 R73 D87 Y90 K94 H101 R104 R106 K107 D108 K109 K112 F113 R114 I116 L117 S120 R121 R124 R127 Y128	G1 R2 M3 H4 G7 K8 G9 I10 S11 S13 A14 I15 P16 S47 G50 R54 T60 R63 K69 M71 R72 D86 Y89 K93 H100 R103 R105 K106 D107 K108 K111 F112 R113 I115 L116 S119 R120 R123 R126 Y127
BS02	rna	Y	H123 K140	H122 K139

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0070181 small ribosomal subunit rRNA binding

Biological Process

• GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0030686 90S preribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6tb3, PDBe:6tb3, PDBj:6tb3
• PDBsum: 6tb3
• PubMed: 32299921
• UniProt: P05756|RS13_YEAST Small ribosomal subunit protein uS15 (Gene Name=RPS13)