Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3RTR

A RING E3-substrate complex poised for ubiquitin-like protein transfer: structural insights into cullin-RING ligases

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0006511	biological_process	ubiquitin-dependent protein catabolic process
A	0031461	cellular_component	cullin-RING ubiquitin ligase complex
A	0031625	molecular_function	ubiquitin protein ligase binding
B	0000165	biological_process	MAPK cascade
B	0000209	biological_process	protein polyubiquitination
B	0004842	molecular_function	ubiquitin-protein transferase activity
B	0005515	molecular_function	protein 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	0006511	biological_process	ubiquitin-dependent protein catabolic process
B	0006513	biological_process	protein monoubiquitination
B	0006974	biological_process	DNA damage response
B	0007283	biological_process	spermatogenesis
B	0008270	molecular_function	zinc ion binding
B	0016567	biological_process	protein ubiquitination
B	0016740	molecular_function	transferase activity
B	0019005	cellular_component	SCF ubiquitin ligase complex
B	0019788	molecular_function	NEDD8 transferase activity
B	0030163	biological_process	protein catabolic process
B	0031146	biological_process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
B	0031461	cellular_component	cullin-RING ubiquitin ligase complex
B	0031462	cellular_component	Cul2-RING ubiquitin ligase complex
B	0031463	cellular_component	Cul3-RING ubiquitin ligase complex
B	0031464	cellular_component	Cul4A-RING E3 ubiquitin ligase complex
B	0031465	cellular_component	Cul4B-RING E3 ubiquitin ligase complex
B	0031466	cellular_component	Cul5-RING ubiquitin ligase complex
B	0031467	cellular_component	Cul7-RING ubiquitin ligase complex
B	0031625	molecular_function	ubiquitin protein ligase binding
B	0032436	biological_process	positive regulation of proteasomal ubiquitin-dependent protein catabolic process
B	0032480	biological_process	negative regulation of type I interferon production
B	0034450	molecular_function	ubiquitin-ubiquitin ligase activity
B	0034644	biological_process	cellular response to UV
B	0042110	biological_process	T cell activation
B	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
B	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
B	0043687	biological_process	post-translational protein modification
B	0045116	biological_process	protein neddylation
B	0045732	biological_process	positive regulation of protein catabolic process
B	0046872	molecular_function	metal ion binding
B	0060090	molecular_function	molecular adaptor activity
B	0061629	molecular_function	RNA polymerase II-specific DNA-binding transcription factor binding
B	0061630	molecular_function	ubiquitin protein ligase activity
B	0061663	molecular_function	NEDD8 ligase activity
B	0062197	biological_process	cellular response to chemical stress
B	0070936	biological_process	protein K48-linked ubiquitination
B	0071230	biological_process	cellular response to amino acid stimulus
B	0090090	biological_process	negative regulation of canonical Wnt signaling pathway
B	0097602	molecular_function	cullin family protein binding
B	0140627	biological_process	ubiquitin-dependent protein catabolic process via the C-end degron rule pathway
B	1900076	biological_process	regulation of cellular response to insulin stimulus
B	1902499	biological_process	positive regulation of protein autoubiquitination
B	1902883	biological_process	negative regulation of response to oxidative stress
B	1904263	biological_process	positive regulation of TORC1 signaling
C	0006511	biological_process	ubiquitin-dependent protein catabolic process
C	0031461	cellular_component	cullin-RING ubiquitin ligase complex
C	0031625	molecular_function	ubiquitin protein ligase binding
D	0000165	biological_process	MAPK cascade
D	0000209	biological_process	protein polyubiquitination
D	0004842	molecular_function	ubiquitin-protein transferase activity
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005654	cellular_component	nucleoplasm
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0006281	biological_process	DNA repair
D	0006511	biological_process	ubiquitin-dependent protein catabolic process
D	0006513	biological_process	protein monoubiquitination
D	0006974	biological_process	DNA damage response
D	0007283	biological_process	spermatogenesis
D	0008270	molecular_function	zinc ion binding
D	0016567	biological_process	protein ubiquitination
D	0016740	molecular_function	transferase activity
D	0019005	cellular_component	SCF ubiquitin ligase complex
D	0019788	molecular_function	NEDD8 transferase activity
D	0030163	biological_process	protein catabolic process
D	0031146	biological_process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
D	0031461	cellular_component	cullin-RING ubiquitin ligase complex
D	0031462	cellular_component	Cul2-RING ubiquitin ligase complex
D	0031463	cellular_component	Cul3-RING ubiquitin ligase complex
D	0031464	cellular_component	Cul4A-RING E3 ubiquitin ligase complex
D	0031465	cellular_component	Cul4B-RING E3 ubiquitin ligase complex
D	0031466	cellular_component	Cul5-RING ubiquitin ligase complex
D	0031467	cellular_component	Cul7-RING ubiquitin ligase complex
D	0031625	molecular_function	ubiquitin protein ligase binding
D	0032436	biological_process	positive regulation of proteasomal ubiquitin-dependent protein catabolic process
D	0032480	biological_process	negative regulation of type I interferon production
D	0034450	molecular_function	ubiquitin-ubiquitin ligase activity
D	0034644	biological_process	cellular response to UV
D	0042110	biological_process	T cell activation
D	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
D	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
D	0043687	biological_process	post-translational protein modification
D	0045116	biological_process	protein neddylation
D	0045732	biological_process	positive regulation of protein catabolic process
D	0046872	molecular_function	metal ion binding
D	0060090	molecular_function	molecular adaptor activity
D	0061629	molecular_function	RNA polymerase II-specific DNA-binding transcription factor binding
D	0061630	molecular_function	ubiquitin protein ligase activity
D	0061663	molecular_function	NEDD8 ligase activity
D	0062197	biological_process	cellular response to chemical stress
D	0070936	biological_process	protein K48-linked ubiquitination
D	0071230	biological_process	cellular response to amino acid stimulus
D	0090090	biological_process	negative regulation of canonical Wnt signaling pathway
D	0097602	molecular_function	cullin family protein binding
D	0140627	biological_process	ubiquitin-dependent protein catabolic process via the C-end degron rule pathway
D	1900076	biological_process	regulation of cellular response to insulin stimulus
D	1902499	biological_process	positive regulation of protein autoubiquitination
D	1902883	biological_process	negative regulation of response to oxidative stress
D	1904263	biological_process	positive regulation of TORC1 signaling
E	0006511	biological_process	ubiquitin-dependent protein catabolic process
E	0031461	cellular_component	cullin-RING ubiquitin ligase complex
E	0031625	molecular_function	ubiquitin protein ligase binding
F	0000165	biological_process	MAPK cascade
F	0000209	biological_process	protein polyubiquitination
F	0004842	molecular_function	ubiquitin-protein transferase activity
F	0005515	molecular_function	protein 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	0006511	biological_process	ubiquitin-dependent protein catabolic process
F	0006513	biological_process	protein monoubiquitination
F	0006974	biological_process	DNA damage response
F	0007283	biological_process	spermatogenesis
F	0008270	molecular_function	zinc ion binding
F	0016567	biological_process	protein ubiquitination
F	0016740	molecular_function	transferase activity
F	0019005	cellular_component	SCF ubiquitin ligase complex
F	0019788	molecular_function	NEDD8 transferase activity
F	0030163	biological_process	protein catabolic process
F	0031146	biological_process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
F	0031461	cellular_component	cullin-RING ubiquitin ligase complex
F	0031462	cellular_component	Cul2-RING ubiquitin ligase complex
F	0031463	cellular_component	Cul3-RING ubiquitin ligase complex
F	0031464	cellular_component	Cul4A-RING E3 ubiquitin ligase complex
F	0031465	cellular_component	Cul4B-RING E3 ubiquitin ligase complex
F	0031466	cellular_component	Cul5-RING ubiquitin ligase complex
F	0031467	cellular_component	Cul7-RING ubiquitin ligase complex
F	0031625	molecular_function	ubiquitin protein ligase binding
F	0032436	biological_process	positive regulation of proteasomal ubiquitin-dependent protein catabolic process
F	0032480	biological_process	negative regulation of type I interferon production
F	0034450	molecular_function	ubiquitin-ubiquitin ligase activity
F	0034644	biological_process	cellular response to UV
F	0042110	biological_process	T cell activation
F	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
F	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
F	0043687	biological_process	post-translational protein modification
F	0045116	biological_process	protein neddylation
F	0045732	biological_process	positive regulation of protein catabolic process
F	0046872	molecular_function	metal ion binding
F	0060090	molecular_function	molecular adaptor activity
F	0061629	molecular_function	RNA polymerase II-specific DNA-binding transcription factor binding
F	0061630	molecular_function	ubiquitin protein ligase activity
F	0061663	molecular_function	NEDD8 ligase activity
F	0062197	biological_process	cellular response to chemical stress
F	0070936	biological_process	protein K48-linked ubiquitination
F	0071230	biological_process	cellular response to amino acid stimulus
F	0090090	biological_process	negative regulation of canonical Wnt signaling pathway
F	0097602	molecular_function	cullin family protein binding
F	0140627	biological_process	ubiquitin-dependent protein catabolic process via the C-end degron rule pathway
F	1900076	biological_process	regulation of cellular response to insulin stimulus
F	1902499	biological_process	positive regulation of protein autoubiquitination
F	1902883	biological_process	negative regulation of response to oxidative stress
F	1904263	biological_process	positive regulation of TORC1 signaling
G	0006511	biological_process	ubiquitin-dependent protein catabolic process
G	0031461	cellular_component	cullin-RING ubiquitin ligase complex
G	0031625	molecular_function	ubiquitin protein ligase binding
H	0000165	biological_process	MAPK cascade
H	0000209	biological_process	protein polyubiquitination
H	0004842	molecular_function	ubiquitin-protein transferase activity
H	0005515	molecular_function	protein 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	0006511	biological_process	ubiquitin-dependent protein catabolic process
H	0006513	biological_process	protein monoubiquitination
H	0006974	biological_process	DNA damage response
H	0007283	biological_process	spermatogenesis
H	0008270	molecular_function	zinc ion binding
H	0016567	biological_process	protein ubiquitination
H	0016740	molecular_function	transferase activity
H	0019005	cellular_component	SCF ubiquitin ligase complex
H	0019788	molecular_function	NEDD8 transferase activity
H	0030163	biological_process	protein catabolic process
H	0031146	biological_process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
H	0031461	cellular_component	cullin-RING ubiquitin ligase complex
H	0031462	cellular_component	Cul2-RING ubiquitin ligase complex
H	0031463	cellular_component	Cul3-RING ubiquitin ligase complex
H	0031464	cellular_component	Cul4A-RING E3 ubiquitin ligase complex
H	0031465	cellular_component	Cul4B-RING E3 ubiquitin ligase complex
H	0031466	cellular_component	Cul5-RING ubiquitin ligase complex
H	0031467	cellular_component	Cul7-RING ubiquitin ligase complex
H	0031625	molecular_function	ubiquitin protein ligase binding
H	0032436	biological_process	positive regulation of proteasomal ubiquitin-dependent protein catabolic process
H	0032480	biological_process	negative regulation of type I interferon production
H	0034450	molecular_function	ubiquitin-ubiquitin ligase activity
H	0034644	biological_process	cellular response to UV
H	0042110	biological_process	T cell activation
H	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
H	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
H	0043687	biological_process	post-translational protein modification
H	0045116	biological_process	protein neddylation
H	0045732	biological_process	positive regulation of protein catabolic process
H	0046872	molecular_function	metal ion binding
H	0060090	molecular_function	molecular adaptor activity
H	0061629	molecular_function	RNA polymerase II-specific DNA-binding transcription factor binding
H	0061630	molecular_function	ubiquitin protein ligase activity
H	0061663	molecular_function	NEDD8 ligase activity
H	0062197	biological_process	cellular response to chemical stress
H	0070936	biological_process	protein K48-linked ubiquitination
H	0071230	biological_process	cellular response to amino acid stimulus
H	0090090	biological_process	negative regulation of canonical Wnt signaling pathway
H	0097602	molecular_function	cullin family protein binding
H	0140627	biological_process	ubiquitin-dependent protein catabolic process via the C-end degron rule pathway
H	1900076	biological_process	regulation of cellular response to insulin stimulus
H	1902499	biological_process	positive regulation of protein autoubiquitination
H	1902883	biological_process	negative regulation of response to oxidative stress
H	1904263	biological_process	positive regulation of TORC1 signaling

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN F 204

Chain	Residue
F	CYS42
F	CYS45
F	HIS80
F	CYS83

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN F 208

Chain	Residue
F	CYS75
F	HIS77
F	CYS94
F	ASP97

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN F 212

Chain	Residue
F	CYS56
F	CYS68
F	HIS82
F	CYS53

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN D 201

Chain	Residue
D	CYS42
D	CYS45
D	HIS80
D	CYS83

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN D 205

Chain	Residue
D	CYS75
D	HIS77
D	CYS94
D	ASP97

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN D 209

Chain	Residue
D	CYS53
D	CYS56
D	CYS68
D	HIS82

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN B 202

Chain	Residue
B	CYS42
B	CYS45
B	HIS80
B	CYS83

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN B 206

Chain	Residue
B	CYS75
B	HIS77
B	CYS94
B	ASP97

site_id	AC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN B 210

Chain	Residue
B	CYS53
B	CYS56
B	CYS68
B	HIS82

site_id	BC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN H 203

Chain	Residue
H	CYS42
H	CYS45
H	HIS80
H	CYS83

site_id	BC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN H 207

Chain	Residue
H	CYS75
H	HIS77
H	CYS94
H	ASP97

site_id	BC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN H 211

Chain	Residue
H	CYS53
H	CYS56
H	CYS68
H	HIS82

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	ILE749-ALA776

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	180
Details	ZN_FING: RING-type => ECO:0000255\|PROSITE-ProRule:PRU00175

Chain	Residue	Details
B	CYS53-ASN98
D	CYS53-ASN98
F	CYS53-ASN98
H	CYS53-ASN98
E	LYS720
G	LYS720

site_id	SWS_FT_FI2
Number of Residues	44
Details	BINDING: BINDING => ECO:0000269\|PubMed:11961546, ECO:0007744\|PDB:1LDJ, ECO:0007744\|PDB:1LDK, ECO:0007744\|PDB:1U6G, ECO:0007744\|PDB:2HYE, ECO:0007744\|PDB:3DPL, ECO:0007744\|PDB:3DQV, ECO:0007744\|PDB:3RTR, ECO:0007744\|PDB:4F52, ECO:0007744\|PDB:4P5O

Chain	Residue	Details
B	CYS42
B	CYS94
B	ASP97
D	CYS42
D	CYS45
D	CYS53
D	CYS56
D	CYS68
D	CYS75
D	HIS77
D	HIS80
B	CYS45
D	HIS82
D	CYS94
D	ASP97
F	CYS42
F	CYS45
F	CYS53
F	CYS56
F	CYS68
F	CYS75
F	HIS77
B	CYS53
F	HIS80
F	HIS82
F	CYS94
F	ASP97
H	CYS42
H	CYS45
H	CYS53
H	CYS56
H	CYS68
H	CYS75
B	CYS56
H	HIS77
H	HIS80
H	HIS82
H	CYS94
H	ASP97
B	CYS68
B	CYS75
B	HIS77
B	HIS80
B	HIS82

site_id	SWS_FT_FI3
Number of Residues	4
Details	BINDING: BINDING => ECO:0000269\|PubMed:11961546, ECO:0007744\|PDB:1LDJ, ECO:0007744\|PDB:1LDK, ECO:0007744\|PDB:1U6G, ECO:0007744\|PDB:2HYE, ECO:0007744\|PDB:3DQV, ECO:0007744\|PDB:3RTR, ECO:0007744\|PDB:4F52, ECO:0007744\|PDB:4P5O

Chain	Residue	Details
B	CYS83
D	CYS83
F	CYS83
H	CYS83

site_id	SWS_FT_FI4
Number of Residues	4
Details	MOD_RES: Phosphothreonine => ECO:0007744\|PubMed:20068231, ECO:0007744\|PubMed:23186163

Chain	Residue	Details
B	THR9
D	THR9
F	THR9
H	THR9

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