3NIL - JenaLib

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Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   THE STRUCTURE OF UBR BOX (RDAA)

Authors :   W. S. Choi, B. -C. Jeong, M. -R. Lee, H. K. Song

Date :   16 Jun 10 (Deposition) - 15 Sep 10 (Release) - 13 Oct 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

Chains :   Asym. Unit : A,B,D,F,X
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: D,X  (1x)
Biol. Unit 4: F  (1x)

Keywords :   E3 Ubiquitin Ligase, Ubr Box, Zinc-Binding Protein, N-End Rule, Ligase, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. S. Choi, B. -C. Jeong, Y. J. Joo, M. -R. Lee, J. Kim, M. J. Eck, H. K. Song
Structural Basis For The Recognition Of N-End Rule Substrates By The Ubr Box Of Ubiquitin Ligases
Nat. Struct. Mol. Biol. V. 17 1175 2010
PubMed-ID: 20835240 | Reference-DOI: 10.1038/NSMB.1907

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE UBR1
	Chains	:	A, B, D, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21(DE3) RIL
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UBR-TYPE DOMAIN, RESIDUES 115-194
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Other Details	:	UBR BOX
	Synonym	:	N-RECOGNIN-1, N-END-RECOGNIZING PROTEIN

Molecule 2 - PEPTIDE RDAA
	Chains	:	X
	Engineered	:	YES
	Other Details	:	CHEMICAL SYNTHESIS
	Synthetic	:	YES

		1	2	3	4	5
Asymmetric Unit	:	A	B	D	F	X
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			D		X
Biological Unit 4 (1x)	:				F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 14)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	ZN	12	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 4 (1, 2)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:123 , CYS A:148 , CYS A:151 , CYS A:175	BINDING SITE FOR RESIDUE ZN A 1
02	AC2	SOFTWARE	HIS A:118 , CYS A:151 , CYS A:177 , CYS A:189	BINDING SITE FOR RESIDUE ZN A 2
03	AC3	SOFTWARE	CYS A:136 , CYS A:139 , HIS A:157 , HIS A:160	BINDING SITE FOR RESIDUE ZN A 3
04	AC4	SOFTWARE	CYS B:123 , CYS B:148 , CYS B:151 , CYS B:175	BINDING SITE FOR RESIDUE ZN B 1
05	AC5	SOFTWARE	HIS B:118 , CYS B:151 , CYS B:177 , CYS B:189	BINDING SITE FOR RESIDUE ZN B 2
06	AC6	SOFTWARE	CYS B:136 , CYS B:139 , HIS B:157 , HIS B:160	BINDING SITE FOR RESIDUE ZN B 3
07	AC7	SOFTWARE	CYS D:123 , CYS D:148 , CYS D:151 , CYS D:175	BINDING SITE FOR RESIDUE ZN D 1
08	AC8	SOFTWARE	HIS D:118 , CYS D:151 , CYS D:177 , CYS D:189	BINDING SITE FOR RESIDUE ZN D 2
09	AC9	SOFTWARE	CYS D:136 , CYS D:139 , HIS D:157 , HIS D:160	BINDING SITE FOR RESIDUE ZN D 3
10	BC1	SOFTWARE	CYS F:123 , CYS F:148 , CYS F:151 , CYS F:175	BINDING SITE FOR RESIDUE ZN F 1
11	BC2	SOFTWARE	HIS F:118 , CYS F:151 , CYS F:177 , CYS F:189	BINDING SITE FOR RESIDUE ZN F 2
12	BC3	SOFTWARE	CYS F:136 , CYS F:139 , ASP F:156 , HIS F:157 , HIS F:160	BINDING SITE FOR RESIDUE ZN F 3
13	BC4	SOFTWARE	THR F:164 , HOH F:407 , HOH F:443	BINDING SITE FOR RESIDUE ACT F 195
14	BC5	SOFTWARE	GLU F:181	BINDING SITE FOR RESIDUE ACT F 196

(no "SS Bond" information available for 3NIL)

(no "Cis Peptide Bond" information available for 3NIL)

(no "SAP(SNP)/Variant" information available for 3NIL)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_UBR	PS51157	Zinc finger UBR-type profile.	UBR1_YEAST	121-194	4	A:121-193 B:121-194 D:121-193 F:121-193

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_UBR	PS51157	Zinc finger UBR-type profile.	UBR1_YEAST	121-194	1	A:121-193 - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_UBR	PS51157	Zinc finger UBR-type profile.	UBR1_YEAST	121-194	1	- B:121-194 - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_UBR	PS51157	Zinc finger UBR-type profile.	UBR1_YEAST	121-194	1	- - D:121-193 -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_UBR	PS51157	Zinc finger UBR-type profile.	UBR1_YEAST	121-194	1	- - - F:121-193

(no "Exon" information available for 3NIL)

Asymmetric 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:81
 aligned with UBR1_YEAST | P19812 from UniProtKB/Swiss-Prot  Length:1950

    Alignment length:81
                                   122       132       142       152       162       172       182       192 
           UBR1_YEAST   113 GDVHKHTGRNCGRKFKIGEPLYRCHECGCDDTCVLCIHCFNPKDHVNHHVCTDICTEFTSGICDCGDEEAWNSPLHCKAEE 193
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................eeeee................hhhhh....eeeee....eee.....hhhhh.....hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------ZF_UBR  PDB: A:121-193 UniProt: 121-194                                   PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 3nil A 113 GSVHKHTGRNCGRKFKIGEPLYRCHECGCDDTCVLCIHCFNPKDHVNHHVCTDICTEFTSGICDCGDEEAWNSPLHCKAEE 193
                                   122       132       142       152       162       172       182       192

Chain B from PDB  Type:PROTEIN  Length:82
 aligned with UBR1_YEAST | P19812 from UniProtKB/Swiss-Prot  Length:1950

    Alignment length:82
                                   122       132       142       152       162       172       182       192  
           UBR1_YEAST   113 GDVHKHTGRNCGRKFKIGEPLYRCHECGCDDTCVLCIHCFNPKDHVNHHVCTDICTEFTSGICDCGDEEAWNSPLHCKAEEQ 194
               SCOP domains ---------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...............eeeee................hhhhhh...eeeee............hhhhh.....hhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------ZF_UBR  PDB: B:121-194 UniProt: 121-194                                    PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 3nil B 113 GSVHKHTGRNCGRKFKIGEPLYRCHECGCDDTCVLCIHCFNPKDHVNHHVCTDICTEFTSGICDCGDEEAWNSPLHCKAEEQ 194
                                   122       132       142       152       162       172       182       192

Chain D from PDB  Type:PROTEIN  Length:81
 aligned with UBR1_YEAST | P19812 from UniProtKB/Swiss-Prot  Length:1950

    Alignment length:81
                                   122       132       142       152       162       172       182       192 
           UBR1_YEAST   113 GDVHKHTGRNCGRKFKIGEPLYRCHECGCDDTCVLCIHCFNPKDHVNHHVCTDICTEFTSGICDCGDEEAWNSPLHCKAEE 193
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................eeeee................hhhhhh...eeeee............hhhhh.....hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------ZF_UBR  PDB: D:121-193 UniProt: 121-194                                   PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 3nil D 113 GSVHKHTGRNCGRKFKIGEPLYRCHECGCDDTCVLCIHCFNPKDHVNHHVCTDICTEFTSGICDCGDEEAWNSPLHCKAEE 193
                                   122       132       142       152       162       172       182       192

Chain F from PDB  Type:PROTEIN  Length:81
 aligned with UBR1_YEAST | P19812 from UniProtKB/Swiss-Prot  Length:1950

    Alignment length:81
                                   122       132       142       152       162       172       182       192 
           UBR1_YEAST   113 GDVHKHTGRNCGRKFKIGEPLYRCHECGCDDTCVLCIHCFNPKDHVNHHVCTDICTEFTSGICDCGDEEAWNSPLHCKAEE 193
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------zf-UBR-3nilF01 F:121-193                                                  Pfam domains (1)
           Pfam domains (2) --------zf-UBR-3nilF02 F:121-193                                                  Pfam domains (2)
           Pfam domains (3) --------zf-UBR-3nilF03 F:121-193                                                  Pfam domains (3)
           Pfam domains (4) --------zf-UBR-3nilF04 F:121-193                                                  Pfam domains (4)
         Sec.struct. author ...................eeeee................hhhhhh...eeeee............hhhhh.....hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------ZF_UBR  PDB: F:121-193 UniProt: 121-194                                   PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 3nil F 113 GSVHKHTGRNCGRKFKIGEPLYRCHECGCDDTCVLCIHCFNPKDHVNHHVCTDICTEFTSGICDCGDEEAWNSPLHCKAEE 193
                                   122       132       142       152       162       172       182       192

Chain X from PDB  Type:PROTEIN  Length:3
                                   
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                 3nil X   1 RDA   3

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 3NIL)

(no "CATH Domain" information available for 3NIL)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: zf-UBR] (12)

Family: zf-UBR (12)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (9)

1a	zf-UBR-3nilF01	F:121-193
1b	zf-UBR-3nilF02	F:121-193
1c	zf-UBR-3nilF03	F:121-193
1d	zf-UBR-3nilF04	F:121-193

Asymmetric Unit(hide GO term definitions)

Chain A,B,D,F (UBR1_YEAST | P19812)

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:0061630	ubiquitin protein ligase activity	Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues.
	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:0006513	protein monoubiquitination	Addition of a single ubiquitin group to a protein.
	GO:0000209	protein polyubiquitination	Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain.
	GO:0016567	protein ubiquitination	The process in which one or more ubiquitin groups are added to a protein.
	GO:0090089	regulation of dipeptide transport	Any process that modulates the rate, frequency or extent of dipeptide transport. Dipeptide transport is the directed movement of a dipeptide, a combination of two amino acids by means of a peptide (-CO-NH-) link, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:1990116	ribosome-associated ubiquitin-dependent protein catabolic process	The chemical reactions and pathways resulting in the breakdown of a protein or peptide encoded by an aberrant message and associated with a stalled ribosome. Degradation is initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the ribosome-associated protein.
	GO:0030433	ubiquitin-dependent ERAD pathway	The series of steps necessary to target endoplasmic reticulum (ER)-resident proteins for degradation by the cytoplasmic proteasome. Begins with recognition of the ER-resident protein, includes retrotranslocation (dislocation) of the protein from the ER to the cytosol, protein ubiquitination necessary for correct substrate transfer, transport of the protein to the proteasome, and ends with degradation of the protein by the cytoplasmic proteasome.
	GO:0071629	ubiquitin-dependent catabolism of misfolded proteins by cytoplasm-associated proteasome	The chemical reactions and pathways resulting in the breakdown of misfolded proteins in the cytoplasm, which are targeted to cytoplasmic proteasomes for degradation.
	GO:0071596	ubiquitin-dependent protein catabolic process via the N-end rule pathway	The chemical reactions and pathways resulting in the breakdown of a protein or peptide covalently tagged with ubiquitin, via the N-end rule pathway. In the N-end rule pathway, destabilizing N-terminal residues (N-degrons) in substrates are recognized by E3 ligases (N-recognins), whereupon the substrates are linked to ubiquitin and then delivered to the proteasome for degradation.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0008540	proteasome regulatory particle, base subcomplex	The subcomplex of the proteasome regulatory particle that directly associates with the proteasome core complex.
	GO:0000151	ubiquitin ligase complex	A protein complex that includes a ubiquitin-protein ligase and enables ubiquitin protein ligase activity. The complex also contains other proteins that may confer substrate specificity on the complex.

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	UBR1_YEAST \| P19812	:	3nih 3nii 3nij 3nik 3nim 3nin 3nis 3nit

3nih	UBR BOX (RIAAA)
3nii	UBR BOX (KIAA)
3nij	UBR BOX (HIAA)
3nik	UBR BOX (REAA)
3nim	UBR BOX (RRAA)
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