Structure of PDB 7nrd Chain LR

Receptor sequence

>7nrdLR (length=183) Species: 559292 (Saccharomyces cerevisiae S288C)

ARYGATSTNPAKSASARGSYLRVSFKNTRETAQAINGWELTKAQKYLEQV
LDHQRAIPFRRFNSSIGRTAQGKEFGVTKARWPAKSVKFVQGLLQNAAAN
AEAKGLDATKLYVSHIQVNQAPKQRRRTYRAHGRINKYESSPSHIELVVT
EKEEAVAKAAEKKVVRLTSRQRGRIAAQKRIAA

3D structure

• PDB: 7nrd Structure of Gcn1 bound to stalled and colliding 80S ribosomes.
• Chain: LR
• Resolution: 4.36 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	LR	R3 Y4 Y21 R23 S25 K27 N28 R30 Q34 K46 Q50 Q55 R56 R62 S65 S66 G68 R69 A71 Q72 K74 E75 K80 R82 W83 P84 K86 N97 A100 N101 K105 H116 Q118 V119 R127 Y130 R131 A132 H133 R135 N137 K138 Y139 E140 S141 R167 T169 S170 R171 Q172 G174 R175 A178 R181 I182	R2 Y3 Y20 R22 S24 K26 N27 R29 Q33 K45 Q49 Q54 R55 R61 S64 S65 G67 R68 A70 Q71 K73 E74 K79 R81 W82 P83 K85 N96 A99 N100 K104 H115 Q117 V118 R126 Y129 R130 A131 H132 R134 N136 K137 Y138 E139 S140 R166 T168 S169 R170 Q171 G173 R174 A177 R180 I181
BS02	rna	LR	R3 Y4 G5 A6 R61 R62 Q118 N120 Q121 A122 P123 H145	R2 Y3 G4 A5 R60 R61 Q117 N119 Q120 A121 P122 H144

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0000448 cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:0030687 preribosome, large subunit precursor
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7nrd, PDBe:7nrd, PDBj:7nrd
• PDBsum: 7nrd
• PubMed: 33790014
• UniProt: P05740|RL17A_YEAST Large ribosomal subunit protein uL22A (Gene Name=RPL17A)