Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4WHV

E3 ubiquitin-protein ligase RNF8 in complex with Ubiquitin-conjugating enzyme E2 N and Polyubiquitin-B

Functional Information from GO Data

Chain	GOid	namespace	contents
B	0000151	cellular_component	ubiquitin ligase complex
B	0000209	biological_process	protein polyubiquitination
B	0000724	biological_process	double-strand break repair via homologous recombination
B	0000729	biological_process	DNA double-strand break processing
B	0003723	molecular_function	RNA binding
B	0004842	molecular_function	ubiquitin-protein transferase activity
B	0005515	molecular_function	protein binding
B	0005524	molecular_function	ATP binding
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0006281	biological_process	DNA repair
B	0006282	biological_process	regulation of DNA repair
B	0006301	biological_process	postreplication repair
B	0006511	biological_process	ubiquitin-dependent protein catabolic process
B	0006513	biological_process	protein monoubiquitination
B	0016567	biological_process	protein ubiquitination
B	0016740	molecular_function	transferase activity
B	0019787	molecular_function	ubiquitin-like protein transferase activity
B	0031371	cellular_component	ubiquitin conjugating enzyme complex
B	0031372	cellular_component	UBC13-MMS2 complex
B	0031625	molecular_function	ubiquitin protein ligase binding
B	0032991	cellular_component	protein-containing complex
B	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
B	0043130	molecular_function	ubiquitin binding
B	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
B	0045739	biological_process	positive regulation of DNA repair
B	0050852	biological_process	T cell receptor signaling pathway
B	0051092	biological_process	positive regulation of NF-kappaB transcription factor activity
B	0061631	molecular_function	ubiquitin conjugating enzyme activity
B	0070062	cellular_component	extracellular exosome
B	0070534	biological_process	protein K63-linked ubiquitination
B	0097027	molecular_function	ubiquitin-protein transferase activator activity
B	0140374	biological_process	antiviral innate immune response
B	1902523	biological_process	positive regulation of protein K63-linked ubiquitination
B	1902533	biological_process	positive regulation of intracellular signal transduction
B	1904262	biological_process	negative regulation of TORC1 signaling
B	2000781	biological_process	positive regulation of double-strand break repair
E	0000151	cellular_component	ubiquitin ligase complex
E	0000209	biological_process	protein polyubiquitination
E	0000724	biological_process	double-strand break repair via homologous recombination
E	0000729	biological_process	DNA double-strand break processing
E	0003723	molecular_function	RNA binding
E	0004842	molecular_function	ubiquitin-protein transferase activity
E	0005515	molecular_function	protein binding
E	0005524	molecular_function	ATP binding
E	0005634	cellular_component	nucleus
E	0005654	cellular_component	nucleoplasm
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0006281	biological_process	DNA repair
E	0006282	biological_process	regulation of DNA repair
E	0006301	biological_process	postreplication repair
E	0006511	biological_process	ubiquitin-dependent protein catabolic process
E	0006513	biological_process	protein monoubiquitination
E	0016567	biological_process	protein ubiquitination
E	0016740	molecular_function	transferase activity
E	0019787	molecular_function	ubiquitin-like protein transferase activity
E	0031371	cellular_component	ubiquitin conjugating enzyme complex
E	0031372	cellular_component	UBC13-MMS2 complex
E	0031625	molecular_function	ubiquitin protein ligase binding
E	0032991	cellular_component	protein-containing complex
E	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
E	0043130	molecular_function	ubiquitin binding
E	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
E	0045739	biological_process	positive regulation of DNA repair
E	0050852	biological_process	T cell receptor signaling pathway
E	0051092	biological_process	positive regulation of NF-kappaB transcription factor activity
E	0061631	molecular_function	ubiquitin conjugating enzyme activity
E	0070062	cellular_component	extracellular exosome
E	0070534	biological_process	protein K63-linked ubiquitination
E	0097027	molecular_function	ubiquitin-protein transferase activator activity
E	0140374	biological_process	antiviral innate immune response
E	1902523	biological_process	positive regulation of protein K63-linked ubiquitination
E	1902533	biological_process	positive regulation of intracellular signal transduction
E	1904262	biological_process	negative regulation of TORC1 signaling
E	2000781	biological_process	positive regulation of double-strand break repair
H	0000151	cellular_component	ubiquitin ligase complex
H	0000209	biological_process	protein polyubiquitination
H	0000724	biological_process	double-strand break repair via homologous recombination
H	0000729	biological_process	DNA double-strand break processing
H	0003723	molecular_function	RNA binding
H	0004842	molecular_function	ubiquitin-protein transferase activity
H	0005515	molecular_function	protein binding
H	0005524	molecular_function	ATP binding
H	0005634	cellular_component	nucleus
H	0005654	cellular_component	nucleoplasm
H	0005737	cellular_component	cytoplasm
H	0005829	cellular_component	cytosol
H	0006281	biological_process	DNA repair
H	0006282	biological_process	regulation of DNA repair
H	0006301	biological_process	postreplication repair
H	0006511	biological_process	ubiquitin-dependent protein catabolic process
H	0006513	biological_process	protein monoubiquitination
H	0016567	biological_process	protein ubiquitination
H	0016740	molecular_function	transferase activity
H	0019787	molecular_function	ubiquitin-like protein transferase activity
H	0031371	cellular_component	ubiquitin conjugating enzyme complex
H	0031372	cellular_component	UBC13-MMS2 complex
H	0031625	molecular_function	ubiquitin protein ligase binding
H	0032991	cellular_component	protein-containing complex
H	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
H	0043130	molecular_function	ubiquitin binding
H	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
H	0045739	biological_process	positive regulation of DNA repair
H	0050852	biological_process	T cell receptor signaling pathway
H	0051092	biological_process	positive regulation of NF-kappaB transcription factor activity
H	0061631	molecular_function	ubiquitin conjugating enzyme activity
H	0070062	cellular_component	extracellular exosome
H	0070534	biological_process	protein K63-linked ubiquitination
H	0097027	molecular_function	ubiquitin-protein transferase activator activity
H	0140374	biological_process	antiviral innate immune response
H	1902523	biological_process	positive regulation of protein K63-linked ubiquitination
H	1902533	biological_process	positive regulation of intracellular signal transduction
H	1904262	biological_process	negative regulation of TORC1 signaling
H	2000781	biological_process	positive regulation of double-strand break repair
K	0000151	cellular_component	ubiquitin ligase complex
K	0000209	biological_process	protein polyubiquitination
K	0000724	biological_process	double-strand break repair via homologous recombination
K	0000729	biological_process	DNA double-strand break processing
K	0003723	molecular_function	RNA binding
K	0004842	molecular_function	ubiquitin-protein transferase activity
K	0005515	molecular_function	protein binding
K	0005524	molecular_function	ATP 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	0006282	biological_process	regulation of DNA repair
K	0006301	biological_process	postreplication repair
K	0006511	biological_process	ubiquitin-dependent protein catabolic process
K	0006513	biological_process	protein monoubiquitination
K	0016567	biological_process	protein ubiquitination
K	0016740	molecular_function	transferase activity
K	0019787	molecular_function	ubiquitin-like protein transferase activity
K	0031371	cellular_component	ubiquitin conjugating enzyme complex
K	0031372	cellular_component	UBC13-MMS2 complex
K	0031625	molecular_function	ubiquitin protein ligase binding
K	0032991	cellular_component	protein-containing complex
K	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
K	0043130	molecular_function	ubiquitin binding
K	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
K	0045739	biological_process	positive regulation of DNA repair
K	0050852	biological_process	T cell receptor signaling pathway
K	0051092	biological_process	positive regulation of NF-kappaB transcription factor activity
K	0061631	molecular_function	ubiquitin conjugating enzyme activity
K	0070062	cellular_component	extracellular exosome
K	0070534	biological_process	protein K63-linked ubiquitination
K	0097027	molecular_function	ubiquitin-protein transferase activator activity
K	0140374	biological_process	antiviral innate immune response
K	1902523	biological_process	positive regulation of protein K63-linked ubiquitination
K	1902533	biological_process	positive regulation of intracellular signal transduction
K	1904262	biological_process	negative regulation of TORC1 signaling
K	2000781	biological_process	positive regulation of double-strand break repair

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	binding site for residue ZN C 501

Chain	Residue
C	CYS418
C	HIS420
C	CYS437
C	CYS440

site_id	AC2
Number of Residues	4
Details	binding site for residue ZN C 502

Chain	Residue
C	CYS403
C	CYS406
C	CYS423
C	CYS426

site_id	AC3
Number of Residues	4
Details	binding site for residue ZN D 501

Chain	Residue
D	HIS420
D	CYS437
D	CYS440
D	CYS418

site_id	AC4
Number of Residues	4
Details	binding site for residue ZN D 502

Chain	Residue
D	CYS403
D	CYS406
D	CYS423
D	CYS426

site_id	AC5
Number of Residues	4
Details	binding site for residue ZN I 501

Chain	Residue
I	CYS418
I	HIS420
I	CYS437
I	CYS440

site_id	AC6
Number of Residues	4
Details	binding site for residue ZN I 502

Chain	Residue
I	CYS403
I	CYS406
I	CYS423
I	CYS426

site_id	AC7
Number of Residues	4
Details	binding site for residue ZN J 501

Chain	Residue
J	CYS418
J	HIS420
J	CYS437
J	CYS440

site_id	AC8
Number of Residues	4
Details	binding site for residue ZN J 502

Chain	Residue
J	CYS403
J	CYS406
J	CYS423
J	CYS426

site_id	AC9
Number of Residues	15
Details	binding site for Di-peptide TYR E 34 and LYS E 74

Chain	Residue
E	PRO27
E	ASP28
E	ASN31
E	ASN31
E	ALA32
E	ARG33
E	PHE35
E	HIS36
E	GLU55
E	LEU56
E	THR73
E	ILE75
E	TRP143
E	TYR147
E	TYR147

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	LYS27-ASP52

site_id	PS00518
Number of Residues	10
Details	ZF_RING_1 Zinc finger RING-type signature. CaHsFCsyCI

Chain	Residue	Details
C	CYS418-ILE427

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	SITE: Interacts with activating enzyme

Chain	Residue	Details
A	ARG54
A	ARG72
F	ARG54
F	ARG72
G	ARG54
G	ARG72
L	ARG54
L	ARG72

site_id	SWS_FT_FI2
Number of Residues	4
Details	SITE: Essential for function

Chain	Residue	Details
A	HIS68
F	HIS68
G	HIS68
L	HIS68

site_id	SWS_FT_FI3
Number of Residues	4
Details	MOD_RES: Phosphoserine; by PINK1 => ECO:0000269\|PubMed:24660806, ECO:0000269\|PubMed:24751536, ECO:0000269\|PubMed:24784582, ECO:0000269\|PubMed:25527291

Chain	Residue	Details
A	SER65
F	SER65
G	SER65
L	SER65
H	LYS92
K	LYS92

site_id	SWS_FT_FI4
Number of Residues	4
Details	MOD_RES: (Microbial infection) ADP-ribosylthreonine => ECO:0000269\|PubMed:32330457

Chain	Residue	Details
A	THR66
F	THR66
G	THR66
L	THR66

site_id	SWS_FT_FI5
Number of Residues	4
Details	MOD_RES: ADP-ribosylglycine => ECO:0000269\|PubMed:28525742

Chain	Residue	Details
A	GLY76
F	GLY76
G	GLY76
L	GLY76

site_id	SWS_FT_FI6
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269\|PubMed:16443603

Chain	Residue	Details
A	LYS6
F	LYS6
G	LYS6
L	LYS6

site_id	SWS_FT_FI7
Number of Residues	8
Details	CROSSLNK: Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)

Chain	Residue	Details
A	GLY76
F	GLY76
G	GLY76
L	GLY76

site_id	SWS_FT_FI8
Number of Residues	8
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269\|PubMed:16443603, ECO:0000269\|PubMed:16543144

Chain	Residue	Details
A	LYS11
A	LYS48
F	LYS11
F	LYS48
G	LYS11
G	LYS48
L	LYS11
L	LYS48

site_id	SWS_FT_FI9
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000305\|PubMed:15466860

Chain	Residue	Details
A	LYS27
F	LYS27
G	LYS27
L	LYS27

site_id	SWS_FT_FI10
Number of Residues	4
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
A	LYS29
F	LYS29
G	LYS29
L	LYS29

site_id	SWS_FT_FI11
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269\|PubMed:25752577

Chain	Residue	Details
A	LYS33
F	LYS33
G	LYS33
L	LYS33

site_id	SWS_FT_FI12
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269\|PubMed:16543144, ECO:0000269\|PubMed:18719106

Chain	Residue	Details
A	LYS63
F	LYS63
G	LYS63
L	LYS63

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)