Structure of PDB 8y0w Chain LL

Receptor sequence

>8y0wLL (length=210) Species: 9606 (Homo sapiens)

APSRNGMVLKPHFHKDWQRRVATWFNQPARKIRRRKARQAKARRIAPRPA
SGPIRPIVRCPTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPR
RRNKSTESLQANVQRLKEYRSKLILFPRKPSAPKKGDSSAEELKLATQLT
GPVMPVRNVYKKEKARVITEEEKNFKAFASLRMARANARLFGIRAKRAKE
AAEQDVEKKK

3D structure

• PDB: 8y0w dormant ribosome with eIF5A, eEF2 and SERBP1
• Chain: LL
• Resolution: 3.4 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	LL	A2 P3 S4 R5 L10 K11 H13 F14 H15 K16 W18 Q28 P29 R31 R35 R36 R39 K42 R56 V59 R60 P62 T63 Y66 H67 R71 R74 L78 K88 R92 D99 P100 R101 R102 R103 R129 K135 R158 N159 K165 R183 R195 K197	A1 P2 S3 R4 L9 K10 H12 F13 H14 K15 W17 Q27 P28 R30 R34 R35 R38 K41 R55 V58 R59 P61 T62 Y65 H66 R70 R73 L77 K87 R91 D98 P99 R100 R101 R102 R128 K134 R157 N158 K164 R182 R194 K196
BS02	rna	LL	A30 R34	A29 R33

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0001824 blastocyst development
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0060348 bone development

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8y0w, PDBe:8y0w, PDBj:8y0w
• PDBsum: 8y0w
• PubMed: 38698775
• UniProt: P26373|RL13_HUMAN Large ribosomal subunit protein eL13 (Gene Name=RPL13)