Structure of PDB 4d5l Chain I

Receptor sequence

>4d5lI (length=207) Species: 9986 (Oryctolagus cuniculus)

GISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGG
NKKYRALRLDVGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCI
VLIDSTPYRQWYESHYALPLGRKKGAKLTPEEEEILNKKRSKKIQKKYDE
RKKNAKISSLLEEQFQQGKLLACIASRPGQCGRADGYVLEGKELEFYLRK
IKARKGK

3D structure

• PDB: 4d5l Cryo-Em of Ribosomal 80S Complexes with Termination Factors Reveals the Translocated Cricket Paralysis Virus Ires.
• Chain: I
• Resolution: 9.0 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	I	G2 I3 R5 W8 K10 R11 R12 T14 K17 R18 Y21 K23 K24 R25 K26 Y27 R31 P32 R41 R42 I43 H44 T45 R47 V48 R49 G50 Y55 L58 L60 V62 S66 C71 C72 T73 R74 K75 S86 N87 V97 K98 N99 S115 H116 K139 S142 K143 I145 Q146 K147 R178 Q181 G183 R184	G1 I2 R4 W7 K9 R10 R11 T13 K16 R17 Y20 K22 K23 R24 K25 Y26 R30 P31 R40 R41 I42 H43 T44 R46 V47 R48 G49 Y54 L57 L59 V61 S65 C70 C71 T72 R73 K74 S85 N86 V96 K97 N98 S114 H115 K138 S141 K142 I144 Q145 K146 R177 Q180 G182 R183

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0006412 translation

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0016020 membrane
• GO:0022626 cytosolic ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4d5l, PDBe:4d5l, PDBj:4d5l
• PDBsum: 4d5l
• PubMed: 25601755
• UniProt: G1TJW1|RS8_RABIT Small ribosomal subunit protein eS8 (Gene Name=RPS8)