Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4ORH

Crystal structure of RNF8 bound to the UBC13/MMS2 heterodimer

Replaces: 4EPO

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000209	biological_process	protein polyubiquitination
A	0000729	biological_process	DNA double-strand break processing
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005737	cellular_component	cytoplasm
A	0006282	biological_process	regulation of DNA repair
A	0006301	biological_process	DNA damage tolerance
A	0016567	biological_process	protein ubiquitination
A	0031371	cellular_component	ubiquitin conjugating enzyme complex
A	0031372	cellular_component	UBC13-MMS2 complex
A	0070062	cellular_component	extracellular exosome
A	0070534	biological_process	protein K63-linked ubiquitination
A	1902523	biological_process	positive regulation of protein K63-linked ubiquitination
A	2000781	biological_process	positive regulation of double-strand break repair
B	0000151	cellular_component	ubiquitin ligase complex
B	0000166	molecular_function	nucleotide binding
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	0001650	cellular_component	fibrillar center
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	DNA damage tolerance
B	0006513	biological_process	protein monoubiquitination
B	0006974	biological_process	DNA damage response
B	0016567	biological_process	protein ubiquitination
B	0016740	molecular_function	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	0000209	biological_process	protein polyubiquitination
E	0000729	biological_process	DNA double-strand break processing
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005654	cellular_component	nucleoplasm
E	0005737	cellular_component	cytoplasm
E	0006282	biological_process	regulation of DNA repair
E	0006301	biological_process	DNA damage tolerance
E	0016567	biological_process	protein ubiquitination
E	0031371	cellular_component	ubiquitin conjugating enzyme complex
E	0031372	cellular_component	UBC13-MMS2 complex
E	0070062	cellular_component	extracellular exosome
E	0070534	biological_process	protein K63-linked ubiquitination
E	1902523	biological_process	positive regulation of protein K63-linked ubiquitination
E	2000781	biological_process	positive regulation of double-strand break repair
F	0000151	cellular_component	ubiquitin ligase complex
F	0000166	molecular_function	nucleotide binding
F	0000209	biological_process	protein polyubiquitination
F	0000724	biological_process	double-strand break repair via homologous recombination
F	0000729	biological_process	DNA double-strand break processing
F	0001650	cellular_component	fibrillar center
F	0003723	molecular_function	RNA binding
F	0004842	molecular_function	ubiquitin-protein transferase activity
F	0005515	molecular_function	protein binding
F	0005524	molecular_function	ATP binding
F	0005634	cellular_component	nucleus
F	0005654	cellular_component	nucleoplasm
F	0005737	cellular_component	cytoplasm
F	0005829	cellular_component	cytosol
F	0006281	biological_process	DNA repair
F	0006282	biological_process	regulation of DNA repair
F	0006301	biological_process	DNA damage tolerance
F	0006513	biological_process	protein monoubiquitination
F	0006974	biological_process	DNA damage response
F	0016567	biological_process	protein ubiquitination
F	0016740	molecular_function	transferase activity
F	0031371	cellular_component	ubiquitin conjugating enzyme complex
F	0031372	cellular_component	UBC13-MMS2 complex
F	0031625	molecular_function	ubiquitin protein ligase binding
F	0032991	cellular_component	protein-containing complex
F	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
F	0043130	molecular_function	ubiquitin binding
F	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
F	0045739	biological_process	positive regulation of DNA repair
F	0050852	biological_process	T cell receptor signaling pathway
F	0051092	biological_process	positive regulation of NF-kappaB transcription factor activity
F	0061631	molecular_function	ubiquitin conjugating enzyme activity
F	0070062	cellular_component	extracellular exosome
F	0070534	biological_process	protein K63-linked ubiquitination
F	0097027	molecular_function	ubiquitin-protein transferase activator activity
F	0140374	biological_process	antiviral innate immune response
F	1902523	biological_process	positive regulation of protein K63-linked ubiquitination
F	1902533	biological_process	positive regulation of intracellular signal transduction
F	1904262	biological_process	negative regulation of TORC1 signaling
F	2000781	biological_process	positive regulation of double-strand break repair
I	0000209	biological_process	protein polyubiquitination
I	0000729	biological_process	DNA double-strand break processing
I	0005515	molecular_function	protein binding
I	0005634	cellular_component	nucleus
I	0005654	cellular_component	nucleoplasm
I	0005737	cellular_component	cytoplasm
I	0006282	biological_process	regulation of DNA repair
I	0006301	biological_process	DNA damage tolerance
I	0016567	biological_process	protein ubiquitination
I	0031371	cellular_component	ubiquitin conjugating enzyme complex
I	0031372	cellular_component	UBC13-MMS2 complex
I	0070062	cellular_component	extracellular exosome
I	0070534	biological_process	protein K63-linked ubiquitination
I	1902523	biological_process	positive regulation of protein K63-linked ubiquitination
I	2000781	biological_process	positive regulation of double-strand break repair
J	0000151	cellular_component	ubiquitin ligase complex
J	0000166	molecular_function	nucleotide binding
J	0000209	biological_process	protein polyubiquitination
J	0000724	biological_process	double-strand break repair via homologous recombination
J	0000729	biological_process	DNA double-strand break processing
J	0001650	cellular_component	fibrillar center
J	0003723	molecular_function	RNA binding
J	0004842	molecular_function	ubiquitin-protein transferase activity
J	0005515	molecular_function	protein binding
J	0005524	molecular_function	ATP binding
J	0005634	cellular_component	nucleus
J	0005654	cellular_component	nucleoplasm
J	0005737	cellular_component	cytoplasm
J	0005829	cellular_component	cytosol
J	0006281	biological_process	DNA repair
J	0006282	biological_process	regulation of DNA repair
J	0006301	biological_process	DNA damage tolerance
J	0006513	biological_process	protein monoubiquitination
J	0006974	biological_process	DNA damage response
J	0016567	biological_process	protein ubiquitination
J	0016740	molecular_function	transferase activity
J	0031371	cellular_component	ubiquitin conjugating enzyme complex
J	0031372	cellular_component	UBC13-MMS2 complex
J	0031625	molecular_function	ubiquitin protein ligase binding
J	0032991	cellular_component	protein-containing complex
J	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
J	0043130	molecular_function	ubiquitin binding
J	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
J	0045739	biological_process	positive regulation of DNA repair
J	0050852	biological_process	T cell receptor signaling pathway
J	0051092	biological_process	positive regulation of NF-kappaB transcription factor activity
J	0061631	molecular_function	ubiquitin conjugating enzyme activity
J	0070062	cellular_component	extracellular exosome
J	0070534	biological_process	protein K63-linked ubiquitination
J	0097027	molecular_function	ubiquitin-protein transferase activator activity
J	0140374	biological_process	antiviral innate immune response
J	1902523	biological_process	positive regulation of protein K63-linked ubiquitination
J	1902533	biological_process	positive regulation of intracellular signal transduction
J	1904262	biological_process	negative regulation of TORC1 signaling
J	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 G 501

Chain	Residue
G	HIS420
G	CYS437
G	CYS440
G	CYS418

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN G 502

Chain	Residue
G	CYS403
G	CYS406
G	CYS423
G	CYS426

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN H 501

Chain	Residue
H	CYS418
H	HIS420
H	CYS437
H	CYS440

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN H 502

Chain	Residue
H	CYS403
H	CYS406
H	CYS423
H	CYS426

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN K 501

Chain	Residue
K	CYS418
K	HIS420
K	CYS437
K	CYS440

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN K 502

Chain	Residue
K	CYS403
K	CYS406
K	CYS423
K	CYS426

site_id	AC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN L 501

Chain	Residue
L	CYS418
L	HIS420
L	CYS437
L	CYS440

site_id	BC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN L 502

Chain	Residue
L	CYS403
L	CYS406
L	CYS423
L	CYS426

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
B	TYR76-LEU91

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	438
Details	Domain: {"description":"UBC core","evidences":[{"source":"PROSITE-ProRule","id":"PRU00388","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	3
Details	Active site: {"description":"Glycyl thioester intermediate","evidences":[{"source":"PROSITE-ProRule","id":"PRU00388","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	3
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	6
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ISG15)","evidences":[{"source":"PubMed","id":"16112642","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16122702","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	190
Details	Zinc finger: {"description":"RING-type","evidences":[{"source":"HAMAP-Rule","id":"MF_03067","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

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