Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

8PQL

K48-linked ubiquitin chain formation with a cullin-RING E3 ligase and Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2-donor UB-acceptor UB-SIL1 peptide

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000082	biological_process	G1/S transition of mitotic cell cycle
A	0004842	molecular_function	ubiquitin-protein transferase activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005730	cellular_component	nucleolus
A	0005829	cellular_component	cytosol
A	0006511	biological_process	ubiquitin-dependent protein catabolic process
A	0016567	biological_process	protein ubiquitination
A	0019005	cellular_component	SCF ubiquitin ligase complex
A	0030163	biological_process	protein catabolic process
A	0030674	molecular_function	protein-macromolecule adaptor activity
A	0030891	cellular_component	VCB complex
A	0031146	biological_process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
A	0031461	cellular_component	cullin-RING ubiquitin ligase complex
A	0031462	cellular_component	Cul2-RING ubiquitin ligase complex
A	0031625	molecular_function	ubiquitin protein ligase binding
A	0044877	molecular_function	protein-containing complex binding
A	0097193	biological_process	intrinsic apoptotic signaling pathway
A	0140627	biological_process	ubiquitin-dependent protein catabolic process via the C-end degron rule pathway
A	0160072	molecular_function	ubiquitin ligase complex scaffold activity
C	0000209	biological_process	protein polyubiquitination
C	0004842	molecular_function	ubiquitin-protein transferase activity
C	0005515	molecular_function	protein binding
C	0005524	molecular_function	ATP binding
C	0005829	cellular_component	cytosol
C	0006511	biological_process	ubiquitin-dependent protein catabolic process
C	0006513	biological_process	protein monoubiquitination
C	0016567	biological_process	protein ubiquitination
C	0016740	molecular_function	transferase activity
C	0019787	molecular_function	ubiquitin-like protein transferase activity
C	0032446	biological_process	protein modification by small protein conjugation
C	0061631	molecular_function	ubiquitin conjugating enzyme activity
C	0070936	biological_process	protein K48-linked ubiquitination
D	0001222	molecular_function	transcription corepressor binding
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005654	cellular_component	nucleoplasm
D	0005829	cellular_component	cytosol
D	0006357	biological_process	regulation of transcription by RNA polymerase II
D	0006367	biological_process	transcription initiation at RNA polymerase II promoter
D	0006511	biological_process	ubiquitin-dependent protein catabolic process
D	0016567	biological_process	protein ubiquitination
D	0030674	molecular_function	protein-macromolecule adaptor activity
D	0031462	cellular_component	Cul2-RING ubiquitin ligase complex
D	0031466	cellular_component	Cul5-RING ubiquitin ligase complex
D	0070449	cellular_component	elongin complex
D	0140958	biological_process	target-directed miRNA degradation
E	0003723	molecular_function	RNA binding
E	0005515	molecular_function	protein binding
E	0005615	cellular_component	extracellular space
E	0005634	cellular_component	nucleus
E	0005654	cellular_component	nucleoplasm
E	0005737	cellular_component	cytoplasm
E	0005739	cellular_component	mitochondrion
E	0005741	cellular_component	mitochondrial outer membrane
E	0005789	cellular_component	endoplasmic reticulum membrane
E	0005829	cellular_component	cytosol
E	0005886	cellular_component	plasma membrane
E	0010008	cellular_component	endosome membrane
E	0016567	biological_process	protein ubiquitination
E	0019941	biological_process	modification-dependent protein catabolic process
E	0030666	cellular_component	endocytic vesicle membrane
E	0031386	molecular_function	protein tag activity
E	0031625	molecular_function	ubiquitin protein ligase binding
E	0031982	cellular_component	vesicle
E	0043229	cellular_component	intracellular organelle
E	0070062	cellular_component	extracellular exosome
G	0001222	molecular_function	transcription corepressor binding
G	0005515	molecular_function	protein binding
G	0005634	cellular_component	nucleus
G	0005654	cellular_component	nucleoplasm
G	0005829	cellular_component	cytosol
G	0006367	biological_process	transcription initiation at RNA polymerase II promoter
G	0006368	biological_process	transcription elongation by RNA polymerase II
G	0016567	biological_process	protein ubiquitination
G	0030891	cellular_component	VCB complex
G	0031462	cellular_component	Cul2-RING ubiquitin ligase complex
G	0031466	cellular_component	Cul5-RING ubiquitin ligase complex
G	0031625	molecular_function	ubiquitin protein ligase binding
G	0032436	biological_process	positive regulation of proteasomal ubiquitin-dependent protein catabolic process
G	0065003	biological_process	protein-containing complex assembly
G	0070449	cellular_component	elongin complex
G	0140958	biological_process	target-directed miRNA degradation
H	0000151	cellular_component	ubiquitin ligase complex
H	0005515	molecular_function	protein binding
H	0005654	cellular_component	nucleoplasm
H	0005829	cellular_component	cytosol
H	0006511	biological_process	ubiquitin-dependent protein catabolic process
H	0016567	biological_process	protein ubiquitination
H	0031462	cellular_component	Cul2-RING ubiquitin ligase complex
H	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
H	0140627	biological_process	ubiquitin-dependent protein catabolic process via the C-end degron rule pathway
H	1990756	molecular_function	ubiquitin-like ligase-substrate adaptor activity
K	0000165	biological_process	MAPK cascade
K	0000209	biological_process	protein polyubiquitination
K	0004842	molecular_function	ubiquitin-protein transferase activity
K	0005515	molecular_function	protein binding
K	0005634	cellular_component	nucleus
K	0005654	cellular_component	nucleoplasm
K	0005737	cellular_component	cytoplasm
K	0005829	cellular_component	cytosol
K	0006281	biological_process	DNA repair
K	0006511	biological_process	ubiquitin-dependent protein catabolic process
K	0006513	biological_process	protein monoubiquitination
K	0006974	biological_process	DNA damage response
K	0007283	biological_process	spermatogenesis
K	0008270	molecular_function	zinc ion binding
K	0016567	biological_process	protein ubiquitination
K	0016740	molecular_function	transferase activity
K	0019005	cellular_component	SCF ubiquitin ligase complex
K	0019788	molecular_function	NEDD8 transferase activity
K	0030163	biological_process	protein catabolic process
K	0031146	biological_process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
K	0031461	cellular_component	cullin-RING ubiquitin ligase complex
K	0031462	cellular_component	Cul2-RING ubiquitin ligase complex
K	0031463	cellular_component	Cul3-RING ubiquitin ligase complex
K	0031464	cellular_component	Cul4A-RING E3 ubiquitin ligase complex
K	0031465	cellular_component	Cul4B-RING E3 ubiquitin ligase complex
K	0031466	cellular_component	Cul5-RING ubiquitin ligase complex
K	0031467	cellular_component	Cul7-RING ubiquitin ligase complex
K	0031625	molecular_function	ubiquitin protein ligase binding
K	0032436	biological_process	positive regulation of proteasomal ubiquitin-dependent protein catabolic process
K	0032480	biological_process	negative regulation of type I interferon production
K	0034450	molecular_function	ubiquitin-ubiquitin ligase activity
K	0034644	biological_process	cellular response to UV
K	0042110	biological_process	T cell activation
K	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
K	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
K	0043687	biological_process	post-translational protein modification
K	0045116	biological_process	protein neddylation
K	0045732	biological_process	positive regulation of protein catabolic process
K	0046872	molecular_function	metal ion binding
K	0060090	molecular_function	molecular adaptor activity
K	0061629	molecular_function	RNA polymerase II-specific DNA-binding transcription factor binding
K	0061630	molecular_function	ubiquitin protein ligase activity
K	0061663	molecular_function	NEDD8 ligase activity
K	0062197	biological_process	cellular response to chemical stress
K	0070936	biological_process	protein K48-linked ubiquitination
K	0071230	biological_process	cellular response to amino acid stimulus
K	0090090	biological_process	negative regulation of canonical Wnt signaling pathway
K	0097602	molecular_function	cullin family protein binding
K	0140627	biological_process	ubiquitin-dependent protein catabolic process via the C-end degron rule pathway
K	1900076	biological_process	regulation of cellular response to insulin stimulus
K	1902499	biological_process	positive regulation of protein autoubiquitination
K	1902883	biological_process	negative regulation of response to oxidative stress
K	1904263	biological_process	positive regulation of TORC1 signaling
U	0003723	molecular_function	RNA binding
U	0005515	molecular_function	protein binding
U	0005615	cellular_component	extracellular space
U	0005634	cellular_component	nucleus
U	0005654	cellular_component	nucleoplasm
U	0005737	cellular_component	cytoplasm
U	0005739	cellular_component	mitochondrion
U	0005741	cellular_component	mitochondrial outer membrane
U	0005789	cellular_component	endoplasmic reticulum membrane
U	0005829	cellular_component	cytosol
U	0005886	cellular_component	plasma membrane
U	0010008	cellular_component	endosome membrane
U	0016567	biological_process	protein ubiquitination
U	0019941	biological_process	modification-dependent protein catabolic process
U	0030666	cellular_component	endocytic vesicle membrane
U	0031386	molecular_function	protein tag activity
U	0031625	molecular_function	ubiquitin protein ligase binding
U	0031982	cellular_component	vesicle
U	0043229	cellular_component	intracellular organelle
U	0070062	cellular_component	extracellular exosome

Functional Information from PROSITE/UniProt

site_id	PS00183
Number of Residues	16
Details	UBC_1 Ubiquitin-conjugating (UBC) active site signature. WHPNIyen.GdVCIsiL

Chain	Residue	Details
C	TRP82-LEU97

site_id	PS00299
Number of Residues	26
Details	UBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGcqleD

Chain	Residue	Details
U	LYS-49-ASP-24
E	LYS27-ASP52
E	LYS103-ASP128
E	LYS179-ASP204
E	LYS255-ASP280
E	LYS331-ASP356
E	LYS407-ASP432
E	LYS483-ASP508
E	LYS559-ASP584
E	LYS635-ASP660
U	LYS27-ASP52
U	LYS103-ASP128
U	LYS179-ASP204
U	LYS255-ASP280
U	LYS331-ASP356
U	LYS407-ASP432
U	LYS483-ASP508
U	LYS559-ASP584

site_id	PS01256
Number of Residues	28
Details	CULLIN_1 Cullin family signature. IKkcIevLIDKqYIeRsqasadeYsYvA

Chain	Residue	Details
A	ILE718-ALA745

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1
Details	MOD_RES: N-acetylmethionine => ECO:0000269\|Ref.6, ECO:0007744\|PubMed:19413330, ECO:0007744\|PubMed:22814378

Chain	Residue	Details
G	MET1
U	ARG-4

site_id	SWS_FT_FI2
Number of Residues	1
Details	MOD_RES: Phosphothreonine => ECO:0000250\|UniProtKB:P62869

Chain	Residue	Details
G	THR84
K	CYS94
K	ASP97
K	CYS45
K	CYS53
K	CYS56
K	CYS68
K	CYS75
K	HIS77
K	HIS80
K	HIS82

site_id	SWS_FT_FI3
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0000250\|UniProtKB:P62869

Chain	Residue	Details
G	SER108
G	SER111

site_id	SWS_FT_FI4
Number of Residues	1
Details	MOD_RES: (Microbial infection) ADP-ribosylthreonine => ECO:0000269\|PubMed:32330457

Chain	Residue	Details
U	THR-10

site_id	SWS_FT_FI5
Number of Residues	1
Details	MOD_RES: ADP-ribosylglycine => ECO:0000269\|PubMed:28525742

Chain	Residue	Details
U	GLY0

site_id	SWS_FT_FI6
Number of Residues	1
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269\|PubMed:16443603

Chain	Residue	Details
U	LYS-70

site_id	SWS_FT_FI7
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)

Chain	Residue	Details
U	GLY0

site_id	SWS_FT_FI8
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269\|PubMed:16443603, ECO:0000269\|PubMed:16543144

Chain	Residue	Details
U	LYS-65
U	CYS-28

site_id	SWS_FT_FI9
Number of Residues	1
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000305\|PubMed:15466860

Chain	Residue	Details
U	LYS-49

site_id	SWS_FT_FI10
Number of Residues	1
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269\|PubMed:16543144, ECO:0000269\|PubMed:25752573, ECO:0000269\|PubMed:25752577, ECO:0000269\|PubMed:34239127

Chain	Residue	Details
U	LYS-47

site_id	SWS_FT_FI11
Number of Residues	1
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269\|PubMed:25752577

Chain	Residue	Details
U	LYS-43

site_id	SWS_FT_FI12
Number of Residues	1
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269\|PubMed:16543144, ECO:0000269\|PubMed:18719106

Chain	Residue	Details
U	LYS-13

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)