Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5AIU

A complex of RNF4-RING domain, Ubc13-Ub (isopeptide crosslink)

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0008270	molecular_function	zinc ion binding
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	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	0033182	biological_process	obsolete regulation of histone ubiquitination
B	0035370	cellular_component	obsolete UBC13-UEV1A 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	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	0033182	biological_process	obsolete regulation of histone ubiquitination
E	0035370	cellular_component	obsolete UBC13-UEV1A 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

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 800

Chain	Residue
A	CYS136
A	CYS139
A	CYS163
A	CYS166

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 801

Chain	Residue
A	CYS158
A	HIS160
A	CYS177
A	CYS180

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 802

Chain	Residue
A	CYS204
A	CYS228
A	CYS231
A	CYS201

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 803

Chain	Residue
A	CYS223
A	HIS225
A	CYS242
A	CYS245

site_id	AC5
Number of Residues	10
Details	BINDING SITE FOR RESIDUE EDO E 1152

Chain	Residue
E	PHE47
E	PHE52
E	LYS74
E	ILE75
E	TYR76
E	ALA140
E	TRP143
E	THR144
E	TYR147
E	ALA148

site_id	AC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO F 1077

Chain	Residue
E	HOH2001
F	PHE45
F	ALA46
F	GLY47
F	HIS68

site_id	AC7
Number of Residues	9
Details	BINDING SITE FOR RESIDUE EDO B 1152

Chain	Residue
B	PHE47
B	PHE52
B	LYS74
B	ILE75
B	TYR76
B	ALA140
B	TRP143
B	THR144
B	TYR147

site_id	AC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO C 1077

Chain	Residue
B	LEU106
C	PHE45
C	ALA46
C	GLY47
C	HIS68

site_id	AC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 1260

Chain	Residue
A	TYR193
A	PRO202
A	HIS225
A	VAL226
A	PHE227
A	THR244

site_id	BC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO B 1153

Chain	Residue
B	LEU15
B	PRO19
B	VAL20
B	ILE23
B	LYS24
B	ALA25

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
C	LYS27-ASP52

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

Chain	Residue	Details
A	CYS158-LEU167
A	CYS223-LEU232

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	SITE: Interacts with activating enzyme

Chain	Residue	Details
C	ARG54
C	ARG72
F	ARG54
F	ARG72

site_id	SWS_FT_FI2
Number of Residues	2
Details	SITE: Essential for function

Chain	Residue	Details
C	HIS68
F	HIS68
A	CYS223
A	HIS225
A	CYS228
A	CYS231
A	CYS242
A	CYS245

site_id	SWS_FT_FI3
Number of Residues	2
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
C	SER65
F	SER65
E	ALA92

site_id	SWS_FT_FI4
Number of Residues	2
Details	MOD_RES: (Microbial infection) ADP-ribosylthreonine => ECO:0000269\|PubMed:32330457

Chain	Residue	Details
C	THR66
F	THR66

site_id	SWS_FT_FI5
Number of Residues	2
Details	MOD_RES: ADP-ribosylglycine => ECO:0000269\|PubMed:28525742

Chain	Residue	Details
C	GLY76
F	GLY76

site_id	SWS_FT_FI6
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269\|PubMed:16443603

Chain	Residue	Details
C	LYS6
F	LYS6

site_id	SWS_FT_FI7
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)

Chain	Residue	Details
C	GLY76
F	GLY76

site_id	SWS_FT_FI8
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269\|PubMed:16443603, ECO:0000269\|PubMed:16543144

Chain	Residue	Details
C	LYS11
C	LYS48
F	LYS11
F	LYS48

site_id	SWS_FT_FI9
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000305\|PubMed:15466860

Chain	Residue	Details
C	LYS27
F	LYS27

site_id	SWS_FT_FI10
Number of Residues	2
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
C	LYS29
F	LYS29

site_id	SWS_FT_FI11
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269\|PubMed:25752577

Chain	Residue	Details
C	LYS33
F	LYS33

site_id	SWS_FT_FI12
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269\|PubMed:16543144, ECO:0000269\|PubMed:18719106

Chain	Residue	Details
C	LYS63
F	LYS63

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