Structure of PDB 8xxn Chain SI

Receptor sequence

>8xxnSI (length=206) Species: 9606 (Homo sapiens)

GISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGG
NKKYRALRLDVGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCI
VLIDSTPYRQWYESHYALPLGRKKGAKLTPEEEEILNKKRSKKIQKKYDE
RKKNAKISSLLEEQFQQGKLLACIASRPGQCGRADGYVLEGKELEFYLRK
IKARKG

3D structure

• PDB: 8xxn Human tumor suppressor PDCD4 directly interacts with ribosomes to repress translation.
• Chain: SI
• Resolution: 3.6 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	SI	G2 I3 R5 N7 H9 K10 R11 R12 K13 T14 K19 Y21 K23 K24 R25 K26 Y27 R31 A33 A34 R42 H44 T45 R47 V48 R49 G50 K53 K54 Y55 R56 L58 N64 S66 T73 K75 S86 K98 N99 K147 Y149 R178 G180 Q181 C182 R184 D186 G187	G1 I2 R4 N6 H8 K9 R10 R11 K12 T13 K18 Y20 K22 K23 R24 K25 Y26 R30 A32 A33 R41 H43 T44 R46 V47 R48 G49 K52 K53 Y54 R55 L57 N63 S65 T72 K74 S85 K97 N98 K146 Y148 R177 G179 Q180 C181 R183 D185 G186

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042274 ribosomal small subunit biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0016020 membrane
• GO:0022626 cytosolic ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0032040 small-subunit processome
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8xxn, PDBe:8xxn, PDBj:8xxn
• PDBsum: 8xxn
• PubMed: 38641729
• UniProt: P62241|RS8_HUMAN Small ribosomal subunit protein eS8 (Gene Name=RPS8)