Structure of PDB 5jup Chain U

Receptor sequence

>5jupU (length=183) Species: 4932 (Saccharomyces cerevisiae)

ARYGATSTNPAKSASARGSYLRVSFKNTRETAQAINGWELTKAQKYLEQV
LDHQRAIPFRRFNSSIGRTAQGKEFGVTKARWPAKSVKFVQGLLQNAAAN
AEAKGLDATKLYVSHIQVNQAPKQRRRTYRAHGRINKYESSPSHIELVVT
EKEEAVAKAAEKKVVRLTSRQRGRIAAQKRIAA

3D structure

• PDB: 5jup Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome.
• Chain: U
• Resolution: 3.5 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	U	R3 Y4 S16 R18 Y21 R23 S25 K27 N28 R30 Q34 Q50 Q55 R56 R62 F63 S65 S66 G68 R69 A71 Q72 K74 G77 T79 K80 R82 W83 P84 A85 K86 N97 A100 N101 Q118 V119 N120 Q121 K124 R127 T129 Y130 R131 A132 H133 G134 R135 I136 N137 K138 Y139 E140 S141 R167 T169 S170 R171 Q172 G174 R175 A178 R181 I182	R2 Y3 S15 R17 Y20 R22 S24 K26 N27 R29 Q33 Q49 Q54 R55 R61 F62 S64 S65 G67 R68 A70 Q71 K73 G76 T78 K79 R81 W82 P83 A84 K85 N96 A99 N100 Q117 V118 N119 Q120 K123 R126 T128 Y129 R130 A131 H132 G133 R134 I135 N136 K137 Y138 E139 S140 R166 T168 S169 R170 Q171 G173 R174 A177 R180 I181
BS02	rna	U	R3 Y4 G5 A6 R30 R61 R62 N120 Q121 P123	R2 Y3 G4 A5 R29 R60 R61 N119 Q120 P122

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:5jup, PDBe:5jup, PDBj:5jup
• PDBsum: 5jup
• PubMed: 27159452
• UniProt: P05740|RL17A_YEAST Large ribosomal subunit protein uL22A (Gene Name=RPL17A)