Structure of PDB 5jup Chain N

Receptor sequence

>5jupN (length=211) Species: 4932 (Saccharomyces cerevisiae)

ARRPARCYRYQKNKPYPKSRYNRAVPDSKIRIYDLGKKKATVDEFPLCVH
LVSNELEQLSSEALEAARICANKYMTTVSGRDAFHLRVRVHPFHVLRINK
MQQGMRGAWGKPHGLAARVDIGQIIFSVRTKDSNKDVVVEGLRRARYKFP
GQQKIILSKKWGFTNLDRPEYLKKREAGEVKDDGAFVKFLSKKGSLENNI
REFPEYFAAQA

3D structure

• PDB: 5jup Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome.
• Chain: N
• 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	N	R3 R4 P5 A6 R7 C8 R10 K13 N14 K15 Y17 Y22 Y34 K39 K40 E63 A64 A67 R88 R90 H92 F94 R98 N100 M115 R116 A118 W119 G120 R154 Y157 K158 P160 G194 A195 F196 K198	R2 R3 P4 A5 R6 C7 R9 K12 N13 K14 Y16 Y21 Y33 K38 K39 E62 A63 A66 R87 R89 H91 F93 R97 N99 M105 R106 A108 W109 G110 R144 Y147 K148 P150 G184 A185 F186 K188
BS02	rna	N	Y11 E56 K202 K203 G204 S205 L206 F217	Y10 E55 K192 K193 G194 S195 L196 F207

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:5jup, PDBe:5jup, PDBj:5jup
• PDBsum: 5jup
• PubMed: 27159452
• UniProt: P41805|RL10_YEAST Large ribosomal subunit protein uL16 (Gene Name=RPL10)