Structure of PDB 8g60 Chain LD

Receptor sequence

>8g60LD (length=293) Species: 9606 (Homo sapiens)

FVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMI
VRVTNRDIICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTG
LLLARRLLNRFGMDKIYEGQVEVTGDEYNVESIDGQPGAFTCYLDAGLAR
TTTGNKVFGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIMGQ
NVADYMRYLMEEDEDAYKKQFSQYIKNSVTPDMMEEMYKKAHAAIRENPV
YEKKPKKEVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAA

3D structure

• PDB: 8g60 mRNA decoding in human is kinetically and structurally distinct from bacteria.
• Chain: LD
• Resolution: 2.54 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	LD	F3 V4 K5 K8 K10 A11 K14 R15 Y16 Q17 K19 R23 G26 T28 D29 Y31 R35 L36 K43 Y44 K48 Y49 F113 P139 G140 F142 Y145 L146 L150 R152 T153 F160 P174 H175 S176 R179 R268 S272 A274 Q275 D278 R279 Q282 K283 S286 R289 A290	F1 V2 K3 K6 K8 A9 K12 R13 Y14 Q15 K17 R21 G24 T26 D27 Y29 R33 L34 K41 Y42 K46 Y47 F111 P137 G138 F140 Y143 L144 L148 R150 T151 F158 P172 H173 S174 R177 R266 S270 A272 Q273 D276 R277 Q280 K281 S284 R287 A288
BS02	rna	LD	K10 F13 K14 Y16 V18 F20 R21 R22 R24 T28 Y30 R33 R50 I52 R54 T56 N57 R58 I61 Q63 I69 G71 D72 M73 I74 Y79 N94 R152 T154 T155 N157 K158 H198 V204 Y207 Y210 Q222 F223 S224 Q225 Y226 Y253 K255 K256 K259 E260 V261 K263 R265 W266 N267 R268 P269 K270 M271 L273 K276 R279 V280 K284	K8 F11 K12 Y14 V16 F18 R19 R20 R22 T26 Y28 R31 R48 I50 R52 T54 N55 R56 I59 Q61 I67 G69 D70 M71 I72 Y77 N92 R150 T152 T153 N155 K156 H196 V202 Y205 Y208 Q220 F221 S222 Q223 Y224 Y251 K253 K254 K257 E258 V259 K261 R263 W264 N265 R266 P267 K268 M269 L271 K274 R277 V278 K282

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:8g60, PDBe:8g60, PDBj:8g60
• PDBsum: 8g60
• PubMed: 37020024
• UniProt: P46777|RL5_HUMAN Large ribosomal subunit protein uL18 (Gene Name=RPL5)