Structure of PDB 8qfd Chain D

Receptor sequence

>8qfdD (length=293) Species: 9606 (Homo sapiens) [Search protein sequence]

FVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMI
VRVTNRDIICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTG
LLLARRLLNRFGMDKIYEGQVEVTGDEYNVESIDGQPGAFTCYLDAGLAR
TTTGNKVFGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIMGQ
NVADYMRYLMEEDEDAYKKQFSQYIKNSVTPDMMEEMYKKAHAAIRENPV
YEKKPKKEVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAA

3D structure

PDB

8qfd The UFM1 E3 ligase recognizes and releases 60S ribosomes from ER translocons

Chain

Resolution

2.2 Å

3D
structure

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Enzymatic activity

Enzyme Commision number

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	D	V6 K10 R15 Y16 Q17 K19 R23 T28 Y31 R35 L36 K43 Y44 K48 F113 M115 P139 G140 F142 Y145 R152 P174 H175 S176 R179 R268 S272 A274 Q275 D278 R279 Q282 S286 R289 A290 R293	V4 K8 R13 Y14 Q15 K17 R21 T26 Y29 R33 L34 K41 Y42 K46 F111 M113 P137 G138 F140 Y143 R150 P172 H173 S174 R177 R266 S270 A272 Q273 D276 R277 Q280 S284 R287 A288 R291
BS02	rna	D	K8 K10 F13 K14 V18 F20 R21 R22 R24 T28 Y30 R33 R50 I52 R54 T56 N57 R58 I61 Q63 I69 G71 D72 M73 I74 N94 R152 T155 N157 K158 H198 N203 Y207 Q222 F223 S224 Q225 Y226 Y253 K255 K256 W266 N267 R268 K270 M271 L273 K277 R279 K284	K6 K8 F11 K12 V16 F18 R19 R20 R22 T26 Y28 R31 R48 I50 R52 T54 N55 R56 I59 Q61 I67 G69 D70 M71 I72 N92 R150 T153 N155 K156 H196 N201 Y205 Q220 F221 S222 Q223 Y224 Y251 K253 K254 W264 N265 R266 K268 M269 L271 K275 R277 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

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Molecular Function

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Biological Process

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Cellular Component

External links

PDB	RCSB:8qfd, PDBe:8qfd, PDBj:8qfd
PDBsum	8qfd
PubMed	38383789
UniProt	P46777\|RL5_HUMAN Large ribosomal subunit protein uL18 (Gene Name=RPL5)

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