2BWF - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STURCTURE OF THE UBL DOMAIN OF DSK2 FROM S. CEREVISIAE

Authors :   E. D. Lowe, N. Hasan, J. -F. Trempe, L. Fonso, M. E. M. Noble, J. A. Endicott, L. N. Johnson, N. R. Brown

Date :   13 Jul 05 (Deposition) - 25 Jan 06 (Release) - 15 Apr 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.15

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Signaling Protein, Ubiquitin, Uba, Signaling Proteins (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. D. Lowe, N. Hasan, J. -F. Trempe, L. Fonso, M. E. M. Noble, J. A. Endicott, L. N. Johnson, N. R. Brown
Structures Of The Dsk2 Ubl And Uba Domains And Their Complex.
Acta Crystallogr. , Sect. D V. 62 177 2006
PubMed-ID: 16421449 | Reference-DOI: 10.1107/S0907444905037777

Molecule 1 - UBIQUITIN-LIKE PROTEIN DSK2
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-KG
	Expression System Strain	:	B834(DE3)PLYSS
	Expression System Taxid	:	562
	Fragment	:	UBL DOMAIN, RESIDUES 1-75
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Other Details	:	UBIQUITIN-LIKE DOMAIN OF DSK2 PROTEIN

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	FMT	2	Ligand/Ion	FORMIC ACID

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	FMT	2	Ligand/Ion	FORMIC ACID

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	FMT	-1	Ligand/Ion	FORMIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:45 , SER A:47 , GLY A:48 , HIS A:69 , HOH A:2078 , HOH A:2079 , MET B:1	BINDING SITE FOR RESIDUE FMT A1076
2	AC2	SOFTWARE	LEU A:25 , GLN A:26 , HOH A:2080 , HOH A:2081 , HOH A:2082 , VAL B:39	BINDING SITE FOR RESIDUE FMT A1077

(no "SS Bond" information available for 2BWF)

(no "Cis Peptide Bond" information available for 2BWF)

(no "SAP(SNP)/Variant" information available for 2BWF)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBIQUITIN_2	PS50053	Ubiquitin domain profile.	DSK2_YEAST	1-77	2	A:1-75 B:1-75
2	UBIQUITIN_1	PS00299	Ubiquitin domain signature.	DSK2_YEAST	28-53	2	A:28-53 B:28-53

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBIQUITIN_2	PS50053	Ubiquitin domain profile.	DSK2_YEAST	1-77	1	A:1-75 -
2	UBIQUITIN_1	PS00299	Ubiquitin domain signature.	DSK2_YEAST	28-53	1	A:28-53 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBIQUITIN_2	PS50053	Ubiquitin domain profile.	DSK2_YEAST	1-77	1	- B:1-75
2	UBIQUITIN_1	PS00299	Ubiquitin domain signature.	DSK2_YEAST	28-53	1	- B:28-53

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YMR276W	1	YMR276W.1	XIII:818826-819947	1122	DSK2_YEAST	1-373	373	2	A:1-75 B:1-75	75 75

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:77
 aligned with DSK2_YEAST | P48510 from UniProtKB/Swiss-Prot  Length:373

    Alignment length:77
                              1                                                                          
                              |      8        18        28        38        48        58        68       
            DSK2_YEAST    - --MSLNIHIKSGQDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKSQP 75
               SCOP domains d2bwfa_ A: automated matches                                                  SCOP domains
               CATH domains 2bwfA00 A:-1-75                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee..eeeeeee....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --UBIQUITIN_2  PDB: A:1-75 UniProt: 1-77                                      PROSITE (1)
                PROSITE (2) -----------------------------UBIQUITIN_1  PDB: A:28-53 ---------------------- PROSITE (2)
               Transcript 1 --Exon 1.1  PDB: A:1-75 UniProt: 1-373 [INCOMPLETE]                           Transcript 1
                  2bwf A -1 LDMSLNIHIKSGQDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKSQP 75
                                     8        18        28        38        48        58        68

Chain B from PDB  Type:PROTEIN  Length:77
 aligned with DSK2_YEAST | P48510 from UniProtKB/Swiss-Prot  Length:373

    Alignment length:77
                              1                                                                          
                              |      8        18        28        38        48        58        68       
            DSK2_YEAST    - --MSLNIHIKSGQDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKSQP 75
               SCOP domains d2bwfb_ B: automated matches                                                  SCOP domains
               CATH domains 2bwfB00 B:-1-75                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................hhhhhhhhhhhhhh.hhhhh..............hhhhh.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --UBIQUITIN_2  PDB: B:1-75 UniProt: 1-77                                      PROSITE (1)
                PROSITE (2) -----------------------------UBIQUITIN_1  PDB: B:28-53 ---------------------- PROSITE (2)
               Transcript 1 --Exon 1.1  PDB: B:1-75 UniProt: 1-373 [INCOMPLETE]                           Transcript 1
                  2bwf B -1 LDMSLNIHIKSGQDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKSQP 75
                                     8        18        28        38        48        58        68

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: beta-Grasp (ubiquitin-like) (1032)

Superfamily: Ubiquitin-like (546)

Family: automated matches (55)

Protein domain: automated matches (55)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (3)

1a	d2bwfa_	A:
1b	d2bwfb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Ubiquitin-like (UB roll) (674)

Homologous Superfamily: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 (286)

Saccharomyces cerevisiae. Organism_taxid: 4932. (2)

1a	2bwfA00	A:-1-75
1b	2bwfB00	B:-1-75

(no "Pfam Domain" information available for 2BWF)

Asymmetric Unit(hide GO term definitions)

Chain A,B (DSK2_YEAST | P48510)

molecular function
	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:0030674	protein binding, bridging	The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
biological process
	GO:0030474	spindle pole body duplication	Construction of a new spindle pole body.
	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.
cellular component
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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Biological Units
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		Biological Unit 2	[ Jena3D ]

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	2bwf
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	DSK2_YEAST \| P48510
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	DSK2_YEAST \| P48510
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UniProtKB/Swiss-Prot
	DSK2_YEAST \| P48510	:	1wr1 2bwb 2bwe 3m63 4un2

1wr1	THE COMPLEX STURCTURE OF DSK2P UBA WITH UBIQUITIN
2bwb	CRYSTAL STURCTURE OF THE UBA DOMAIN OF DSK2 FROM S. CEREVISIAE
2bwe	THE CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE UBA AND UBL DOMAINS OF DSK2

Description

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