4DBG - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HOIL-1L-UBL COMPLEXED WITH A HOIP-UBA DERIVATIVE

Authors :   H. Yagi, T. Hiromoto, T. Mizushima, E. Kurimoto, K. Kato

Date :   15 Jan 12 (Deposition) - 04 Apr 12 (Release) - 16 May 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.71

Chains :   Asym./Biol. Unit : A,B

Keywords :   Ubiquitin Fold, Ubiquitination, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Yagi, K. Ishimoto, T. Hiromoto, H. Fujita, T. Mizushima, Y. Uekusa, M. Yagi-Utsumi, E. Kurimoto, M. Noda, S. Uchiyama, F. Tokunaga, K. Iwai, K. Kato
A Non-Canonical Uba-Ubl Interaction Forms The Linear-Ubiquitin-Chain Assembly Complex
Embo Rep. V. 13 462 2012
PubMed-ID: 22430200 | Reference-DOI: 10.1038/EMBOR.2012.24

Molecule 1 - RANBP-TYPE AND C3HC4-TYPE ZINC FINGER-CONTAINING PROTEIN 1
	Chains	:	A
	EC Number	:	6.3.2.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-28A
	Expression System Strain	:	BL21-CODONPLUS(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UB-LIKE DOMAIN, RESIDUES 37-137
	Gene	:	RBCK1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HBV-ASSOCIATED FACTOR 4, HEME-OXIDIZED IRP2 UBIQUITIN LIGASE 1, HOIL-1, HEPATITIS B VIRUS X-ASSOCIATED PROTEIN 4, RING FINGER PROTEIN 54, UBIQUITIN-CONJUGATING ENZYME 7-INTERACTING PROTEIN 3

Molecule 2 - RING FINGER PROTEIN 31
	Chains	:	B
	EC Number	:	6.3.2.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX6P-1
	Expression System Strain	:	BL21-CODONPLUS(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UB-ASSOCIATED DOMAIN, RESIDUES 480-636
	Gene	:	RNF31
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HOIL-1-INTERACTING PROTEIN, HOIP, ZINC IN-BETWEEN-RING- FINGER UBIQUITIN-ASSOCIATED DOMAIN PROTEIN

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 4DBG)

(no "Site" information available for 4DBG)

Asymmetric/Biological Unit

No.	Residues
1	B:504	-	B:551

(no "Cis Peptide Bond" information available for 4DBG)

(no "SAP(SNP)/Variant" information available for 4DBG)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBIQUITIN_2	PS50053	Ubiquitin domain profile.	HOIL1_HUMAN	55-122	1	A:55-122
2	UBA	PS50030	Ubiquitin-associated domain (UBA) profile.	RNF31_HUMAN	564-615	1	B:564-615

Asymmetric/Biological Unit (6, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1c	ENST00000324103	1c	ENSE00001872297	chr14:24616739-24617099	361	RNF31_HUMAN	1-64	64	0	-	-
1.2c	ENST00000324103	2c	ENSE00001361365	chr14:24617185-24617331	147	RNF31_HUMAN	65-113	49	0	-	-
1.3	ENST00000324103	3	ENSE00001032020	chr14:24617467-24617622	156	RNF31_HUMAN	114-165	52	0	-	-
1.5	ENST00000324103	5	ENSE00001361361	chr14:24617851-24617910	60	RNF31_HUMAN	166-185	20	0	-	-
1.6	ENST00000324103	6	ENSE00001032013	chr14:24618010-24618085	76	RNF31_HUMAN	186-211	26	0	-	-
1.7	ENST00000324103	7	ENSE00001032019	chr14:24618615-24618792	178	RNF31_HUMAN	211-270	60	0	-	-
1.8	ENST00000324103	8	ENSE00001032022	chr14:24619270-24619657	388	RNF31_HUMAN	270-399	130	0	-	-
1.9	ENST00000324103	9	ENSE00001032016	chr14:24619807-24620097	291	RNF31_HUMAN	400-496	97	1	B:482-496	15
1.10	ENST00000324103	10	ENSE00000889364	chr14:24620340-24620588	249	RNF31_HUMAN	497-579	83	1	B:497-579	83
1.11a	ENST00000324103	11a	ENSE00001617333	chr14:24620694-24620879	186	RNF31_HUMAN	580-641	62	1	B:580-627	48
1.12	ENST00000324103	12	ENSE00001780213	chr14:24620995-24621201	207	RNF31_HUMAN	642-710	69	0	-	-
1.13	ENST00000324103	13	ENSE00001662886	chr14:24624366-24624539	174	RNF31_HUMAN	711-768	58	0	-	-
1.14	ENST00000324103	14	ENSE00001793277	chr14:24624623-24624721	99	RNF31_HUMAN	769-801	33	0	-	-
1.15	ENST00000324103	15	ENSE00001759230	chr14:24624812-24624901	90	RNF31_HUMAN	802-831	30	0	-	-
1.16a	ENST00000324103	16a	ENSE00001755858	chr14:24626499-24626613	115	RNF31_HUMAN	832-870	39	0	-	-
1.17	ENST00000324103	17	ENSE00001772571	chr14:24626729-24626847	119	RNF31_HUMAN	870-909	40	0	-	-
1.18	ENST00000324103	18	ENSE00001787690	chr14:24627107-24627220	114	RNF31_HUMAN	910-947	38	0	-	-
1.19	ENST00000324103	19	ENSE00001696970	chr14:24627351-24627408	58	RNF31_HUMAN	948-967	20	0	-	-
1.20	ENST00000324103	20	ENSE00001639274	chr14:24629073-24629169	97	RNF31_HUMAN	967-999	33	0	-	-
1.21	ENST00000324103	21	ENSE00001686595	chr14:24629448-24629616	169	RNF31_HUMAN	999-1055	57	0	-	-
1.22b	ENST00000324103	22b	ENSE00001926486	chr14:24629729-24629866	138	RNF31_HUMAN	1056-1072	17	0	-	-

2.2b	ENST00000356286	2b	ENSE00001491331	chr20:388697-389423	727	HOIL1_HUMAN	1-8	8	0	-	-
2.3b	ENST00000356286	3b	ENSE00001621542	chr20:390525-390669	145	HOIL1_HUMAN	8-56	49	1	A:52-56	5
2.6	ENST00000356286	6	ENSE00001604688	chr20:398170-398263	94	HOIL1_HUMAN	56-87	32	1	A:56-87	32
2.7c	ENST00000356286	7c	ENSE00001665019	chr20:398376-398574	199	HOIL1_HUMAN	88-154	67	1	A:88-133	46
2.8	ENST00000356286	8	ENSE00001678391	chr20:399991-400112	122	HOIL1_HUMAN	154-194	41	0	-	-
2.9c	ENST00000356286	9c	ENSE00001609465	chr20:400202-400375	174	HOIL1_HUMAN	195-252	58	0	-	-
2.10b	ENST00000356286	10b	ENSE00001226965	chr20:401515-401675	161	HOIL1_HUMAN	253-306	54	0	-	-
2.11b	ENST00000356286	11b	ENSE00001703252	chr20:402771-402882	112	HOIL1_HUMAN	306-343	38	0	-	-
2.12	ENST00000356286	12	ENSE00001755728	chr20:407957-408136	180	HOIL1_HUMAN	344-403	60	0	-	-
2.13a	ENST00000356286	13a	ENSE00001802312	chr20:409135-409233	99	HOIL1_HUMAN	404-436	33	0	-	-
2.13c	ENST00000356286	13c	ENSE00001772865	chr20:409595-409738	144	HOIL1_HUMAN	437-484	48	0	-	-
2.14b	ENST00000356286	14b	ENSE00001804805	chr20:410994-411610	617	HOIL1_HUMAN	485-510	26	0	-	-

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:82
 aligned with HOIL1_HUMAN | Q9BYM8 from UniProtKB/Swiss-Prot  Length:510

    Alignment length:82
                                    61        71        81        91       101       111       121       131  
          HOIL1_HUMAN    52 TQDIRLWVSVEDAQMHTVTIWLTVRPDMTVASLKDMVFLDYGFPPVLQQWVIGQRLARDQETLHSHGVRQNGDSAYLYLLSA 133
               SCOP domains ---------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee.....eeeeeee....hhhhhhhhhhhhhh.hhh.eeeee..eee.....hhhhh......eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---UBIQUITIN_2  PDB: A:55-122 UniProt: 55-122                          ----------- PROSITE
           Transcript 2 (1) 2.3b -------------------------------Exon 2.7c  PDB: A:88-133 UniProt: 88-154       Transcript 2 (1)
           Transcript 2 (2) ----Exon 2.6  PDB: A:56-87          ---------------------------------------------- Transcript 2 (2)
                 4dbg A  52 TQDIRLWVSVEDAQMHTVTIWLTVRPDMTVASLKDMVFLDYGFPPVLQQWVIGQRLARDQETLHSHGVRQNGDSAYLYLLSA 133
                                    61        71        81        91       101       111       121       131

Chain B from PDB  Type:PROTEIN  Length:146
 aligned with RNF31_HUMAN | Q96EP0 from UniProtKB/Swiss-Prot  Length:1072

    Alignment length:146
                                   491       501       511       521       531       541       551       561       571       581       591       601       611       621      
          RNF31_HUMAN   482 DKMREEGLQLVSMIREGEAAGACPEEIFSALQYSGTEVPLQWLRSELPYVLEMVAELAGQQDPGLGAFSCQEARRAWLDRHGNLDEAVEECVRTRRRKVQELQSLGFGPEEGSLQALFQHGGDVSRALTELQRQRLEPFRQRLWDS 627
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.........hhhhhhhhhhhhh...hhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------UBA  PDB: B:564-615 UniProt: 564-615                ------------ PROSITE
               Transcript 1 Exon 1.9       Exon 1.10  PDB: B:497-579 UniProt: 497-579                                         Exon 1.11a  PDB: B:580-627 UniProt: 580-641      Transcript 1
                 4dbg B 482 DKMREEGLQLVSMIREGEAAGACPEEIFSALQYSGTEVPLQWLRSELPYVLEMVAELAGQQDPGLGAFSCQEARRAWLDRHGNLDEAVEECVRTRRRKVQELQSLGFGPEEGSLQALFQHGGDVSRALTELQRQRLEPFRQRLWDS 627
                                   491       501       511       521       531       541       551       561       571       581       591       601       611       621

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 4DBG)

(no "CATH Domain" information available for 4DBG)

(no "Pfam Domain" information available for 4DBG)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (HOIL1_HUMAN | Q9BYM8)

molecular function
	GO:0003690	double-stranded DNA binding	Interacting selectively and non-covalently with double-stranded DNA.
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0005080	protein kinase C binding	Interacting selectively and non-covalently with protein kinase C.
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	GO:0043130	ubiquitin binding	Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
	GO:0004842	ubiquitin-protein transferase activity	Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0007249	I-kappaB kinase/NF-kappaB signaling	The process in which a signal is passed on to downstream components within the cell through the I-kappaB-kinase (IKK)-dependent activation of NF-kappaB. The cascade begins with activation of a trimeric IKK complex (consisting of catalytic kinase subunits IKKalpha and/or IKKbeta, and the regulatory scaffold protein NEMO) and ends with the regulation of transcription of target genes by NF-kappaB. In a resting state, NF-kappaB dimers are bound to I-kappaB proteins, sequestering NF-kappaB in the cytoplasm. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing the NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription.
	GO:0050852	T cell receptor signaling pathway	A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
	GO:0032088	negative regulation of NF-kappaB transcription factor activity	Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor NF-kappaB.
	GO:0060546	negative regulation of necroptotic process	Any process that decreases the rate, frequency or extent of a necroptotic process, a necrotic cell death process that results from the activation of endogenous cellular processes, such as signaling involving death domain receptors or Toll-like receptors.
	GO:0043123	positive regulation of I-kappaB kinase/NF-kappaB signaling	Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
	GO:0042346	positive regulation of NF-kappaB import into nucleus	Any process that activates or increases the frequency, rate or extent of transfer of NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters, from the cytoplasm into the nucleus, across the nuclear membrane.
	GO:0051092	positive regulation of NF-kappaB transcription factor activity	Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
	GO:0043065	positive regulation of apoptotic process	Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
	GO:2001238	positive regulation of extrinsic apoptotic signaling pathway	Any process that activates or increases the frequency, rate or extent of extrinsic apoptotic signaling pathway.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0043161	proteasome-mediated ubiquitin-dependent protein catabolic process	The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
	GO:0097039	protein linear polyubiquitination	A protein ubiquitination process in which a linear polymer of ubiquitin, formed by the amino-terminal methionine (M1) of one ubiquitin molecule and by the carboxy-terminal glycine (G76) of the next, is added to a protein.
	GO:0000209	protein polyubiquitination	Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain.
	GO:0010803	regulation of tumor necrosis factor-mediated signaling pathway	Any process that modulates the rate or extent of the tumor necrosis factor-mediated signaling pathway. The tumor necrosis factor-mediated signaling pathway is the series of molecular signals generated as a consequence of tumor necrosis factor binding to a cell surface receptor.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0071797	LUBAC complex	A ubiquitin ligase complex that catalyzes linear head-to-tail polyubiquitin conjugation on its targets. In human the complex consists of RBCK1, RNF31 and SHARPIN, and has an MW of approximately 600 kDa, suggesting a heteromultimeric assembly of its subunits. LUBAC stands for Linear Ubiquitin Chain Assembly Complex.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Chain B (RNF31_HUMAN | Q96EP0)

molecular function
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0043130	ubiquitin binding	Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
	GO:0031625	ubiquitin protein ligase binding	Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
	GO:0004842	ubiquitin-protein transferase activity	Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0023035	CD40 signaling pathway	A series of molecular signals initiated by the binding of the cell surface receptor CD40 to one of its physiological ligands, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0007249	I-kappaB kinase/NF-kappaB signaling	The process in which a signal is passed on to downstream components within the cell through the I-kappaB-kinase (IKK)-dependent activation of NF-kappaB. The cascade begins with activation of a trimeric IKK complex (consisting of catalytic kinase subunits IKKalpha and/or IKKbeta, and the regulatory scaffold protein NEMO) and ends with the regulation of transcription of target genes by NF-kappaB. In a resting state, NF-kappaB dimers are bound to I-kappaB proteins, sequestering NF-kappaB in the cytoplasm. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing the NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription.
	GO:0050852	T cell receptor signaling pathway	A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
	GO:0043123	positive regulation of I-kappaB kinase/NF-kappaB signaling	Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
	GO:0051092	positive regulation of NF-kappaB transcription factor activity	Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
	GO:1903955	positive regulation of protein targeting to mitochondrion	Any process that activates or increases the frequency, rate or extent of protein targeting to mitochondrion.
	GO:0097039	protein linear polyubiquitination	A protein ubiquitination process in which a linear polymer of ubiquitin, formed by the amino-terminal methionine (M1) of one ubiquitin molecule and by the carboxy-terminal glycine (G76) of the next, is added to a protein.
	GO:0000209	protein polyubiquitination	Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain.
	GO:0010803	regulation of tumor necrosis factor-mediated signaling pathway	Any process that modulates the rate or extent of the tumor necrosis factor-mediated signaling pathway. The tumor necrosis factor-mediated signaling pathway is the series of molecular signals generated as a consequence of tumor necrosis factor binding to a cell surface receptor.
cellular component
	GO:0035631	CD40 receptor complex	A protein complex that contains at least CD40 (a cell surface receptor of the tumour necrosis factor receptor (TNFR) superfamily), and other signaling molecules.
	GO:0071797	LUBAC complex	A ubiquitin ligase complex that catalyzes linear head-to-tail polyubiquitin conjugation on its targets. In human the complex consists of RBCK1, RNF31 and SHARPIN, and has an MW of approximately 600 kDa, suggesting a heteromultimeric assembly of its subunits. LUBAC stands for Linear Ubiquitin Chain Assembly Complex.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0009898	cytoplasmic side of plasma membrane	The leaflet the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric/Biological Unit
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