Structure of PDB 6ip6 Chain 1G

Receptor sequence

>6ip61G (length=293) Species: 9606 (Homo sapiens)

GFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRM
IVRVTNRDIICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCT
GLLLARRLLNRFGMDKIYEGQVEVTGDEYNVESIDGQPGAFTCYLDAGLA
RTTTGNKVFGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIMG
QNVADYMRYLMEEDEDAYKKQFSQYIKNSVTPDMMEEMYKKAHAAIRENP
VYEKKPKKEVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERA

3D structure

• PDB: 6ip6 HCV IRES Captures an Actively Translating 80S Ribosome.
• Chain: 1G
• Resolution: 4.5 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	1G	G2 F3 V4 K5 K8 K10 Y12 K14 Y16 K19 R23 D29 Y31 R35 L36 K43 Y44 T46 K48 F113 P139 G140 F142 Y145 L146 T153 F160 H175 S176 R179 R268 Q275 D278 Q282 S286 F287 R289	G1 F2 V3 K4 K7 K9 Y11 K13 Y15 K18 R22 D28 Y30 R34 L35 K42 Y43 T45 K47 F112 P138 G139 F141 Y144 L145 T152 F159 H174 S175 R178 R267 Q274 D277 Q281 S285 F286 R288
BS02	rna	1G	K10 F13 V18 F20 R21 R22 R24 K27 T28 Y30 R33 R50 R54 T56 N57 R58 Q63 I69 D72 I74 Y79 N94 R152 N157 K158 N203 Y207 Q222 S224 Q225 Y226 Y253 K255 K258 E260 V261 K262 K263 K264 R265 W266 N267 R268 K270 M271 L273 K276 R279	K9 F12 V17 F19 R20 R21 R23 K26 T27 Y29 R32 R49 R53 T55 N56 R57 Q62 I68 D71 I73 Y78 N93 R151 N156 K157 N202 Y206 Q221 S223 Q224 Y225 Y252 K254 K257 E259 V260 K261 K262 K263 R264 W265 N266 R267 K269 M270 L272 K275 R278

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003730 mRNA 3'-UTR binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding
• GO:0031625 ubiquitin protein ligase binding
• GO:0048027 mRNA 5'-UTR binding
• GO:1990948 ubiquitin ligase inhibitor activity

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0010628 positive regulation of gene expression
• GO:0042273 ribosomal large subunit biogenesis
• GO:0045727 positive regulation of translation
• GO:0050821 protein stabilization
• GO:1901796 regulation of signal transduction by p53 class mediator
• GO:1904667 negative regulation of ubiquitin protein ligase activity
• GO:2000059 negative regulation of ubiquitin-dependent protein catabolic process
• GO:2000435 negative regulation of protein neddylation

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:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0032991 protein-containing complex
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6ip6, PDBe:6ip6, PDBj:6ip6
• PDBsum: 6ip6
• PubMed: 31080011
• UniProt: P46777|RL5_HUMAN Large ribosomal subunit protein uL18 (Gene Name=RPL5)