Structure of PDB 6tb3 Chain BD

Receptor sequence

>6tb3BD (length=218) Species: 559292 (Saccharomyces cerevisiae S288C)

ARRPARCYRYQKNKPYPKSRYNRAVPDSKIRIYDLGKKKATVDEFPLCVH
LVSNELEQLSSEALEAARICANKYMTTVSGRDAFHLRVRVHPFHVLRINK
MLSCAGADRLQQGMRGAWGKPHGLAARVDIGQIIFSVRTKDSNKDVVVEG
LRRARYKFPGQQKIILSKKWGFTNLDRPEYLKKREAGEVKDDGAFVKFLS
KKGSLENNIREFPEYFAA

3D structure

• PDB: 6tb3 The Ccr4-Not complex monitors the translating ribosome for codon optimality.
• Chain: BD
• 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	BD	R110 L111	R109 L110
BS02	rna	BD	R3 R4 A6 R7 K13 N14 K15 Y17 R21 Y22 R24 D35 K39 K40 E63 A64 R90 H92 F94 R98 G107 D109 R110 Q112 Q113 M115 R116 A118 W119 G120 Q133 R154 Y157 K158 P160 D193 G194 F196 K198	R2 R3 A5 R6 K12 N13 K14 Y16 R20 Y21 R23 D34 K38 K39 E62 A63 R89 H91 F93 R97 G106 D108 R109 Q111 Q112 M114 R115 A117 W118 G119 Q132 R153 Y156 K157 P159 D192 G193 F195 K197
BS03	rna	BD	Y11 E56 K202 K203 G204 L206 N209	Y10 E55 K201 K202 G203 L205 N208

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0006415 translational termination

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: P41805|RL10_YEAST Large ribosomal subunit protein uL16 (Gene Name=RPL10)