Structure of PDB 6ip8 Chain 2B

Receptor sequence

>6ip82B (length=241) Species: 9606 (Homo sapiens)

KVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQRAILYKRLK
VPPAINQFTQALDRQTATQLLKLAHKYRPETKQEKKQRLLARAEKKAAGK
GDVPTKRPPVLRAGVNTVTTLVENKKAQLVVIAHDVDPIELVVFLPALCR
KMGVPYCIIKGKARLGRLVHRKTCTTVAFTQVNSEDKGALAKLVEAIRTN
YNDRYDEIRRHWGGNVLGPKSVARIAKLEKAKAKELATKLG

3D structure

• PDB: 6ip8 HCV IRES Captures an Actively Translating 80S Ribosome.
• Chain: 2B
• Resolution: 3.9 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	2B	E33 K34 R35 K37 N38 F39 I41 Q43 I45 Q46 K48 R53 F54 K56 P58 R59 Y60 I69 K72 R73 K75 K110 R113 R132 P133 A138 G139 V140 N141 T142 V161 D162 A188 R196 K197 T198 C199 T200 P244 K245	E8 K9 R10 K12 N13 F14 I16 Q18 I20 Q21 K23 R28 F29 K31 P33 R34 Y35 I44 K47 R48 K50 K85 R88 R107 P108 A113 G114 V115 N116 T117 V136 D137 A163 R171 K172 T173 C174 T175 P219 K220
BS02	rna	2B	T52 Y60 Q64 R65 R89 D160 K185 R189	T27 Y35 Q39 R40 R64 D135 K160 R164

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0045296 cadherin binding

Biological Process

• GO:0000470 maturation of LSU-rRNA
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042254 ribosome biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6ip8, PDBe:6ip8, PDBj:6ip8
• PDBsum: 6ip8
• PubMed: 31080011
• UniProt: P62424|RL7A_HUMAN Large ribosomal subunit protein eL8 (Gene Name=RPL7A)