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Title :   2DZI/SOLUTION STRUCTURE OF THE N-TERMINAL UBIQUITIN-LIKE DOMAIN IN HUMAN UBIQUITIN-LIKE PROTEIN 4A (GDX)

Authors :   C. Zhao, M. Sato, S. Koshiba, S. Watanabe, T. Harada, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   29 Sep 06 (Deposition) - 29 Mar 07 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Ubiquitin-Like Protein 4A, Gdx, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Zhao, M. Sato, S. Koshiba, S. Watanabe, T. Harada, T. Kigawa, S. Yokoyama
2Dzi/Solution Structure Of The N-Terminal Ubiquitin-Like Domain In Human Ubiquitin-Like Protein 4A (Gdx)
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - UBIQUITIN-LIKE PROTEIN 4A
	Chains	:	A
	Engineered	:	YES
	Expression System Plasmid	:	P060227-19
	Expression System Vector Type	:	PLASMID
	Fragment	:	UBIQUITIN-LIKE DOMAIN
	Gene	:	UBL4A, DXS254E, GDX, UBL4
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS
	Synonym	:	UBIQUITIN-LIKE PROTEIN GDX


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2DZI)

(no "Site" information available for 2DZI)

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

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

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

NMR Structure (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBIQUITIN_2	PS50053	Ubiquitin domain profile.	UBL4A_HUMAN	1-72	1	A:8-79
2	UBIQUITIN_1	PS00299	Ubiquitin domain signature.	UBL4A_HUMAN	27-52	1	A:34-59

NMR Structure (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000369660	1a	ENSE00001929885	X:153715009-153714876	134	UBL4A_HUMAN	1-16	16	1	A:8-23	16
1.2a	ENST00000369660	2a	ENSE00000678584	X:153714672-153714567	106	UBL4A_HUMAN	17-52	36	1	A:24-59	36
1.2e	ENST00000369660	2e	ENSE00001620198	X:153714318-153714110	209	UBL4A_HUMAN	52-121	70	1	A:59-81	23
1.3e	ENST00000369660	3e	ENSE00001450568	X:153713988-153712056	1933	UBL4A_HUMAN	122-157	36	0	-	-

NMR Structure

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

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
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Chain A from PDB  Type:PROTEIN  Length:81
 aligned with UBL4A_HUMAN | P11441 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:81
                                   1                                                                         
                                   | 3        13        23        33        43        53        63        73 
           UBL4A_HUMAN    - -------MQLTVKALQGRECSLQVPEDELVSTLKQLVSEKLNVPVRQQRLLFKGKALADGKRLSDYSIGPNSKLNLVVKPL 74
               SCOP domains d2dzia_ A: automated matches                                                      SCOP domains
               CATH domains 2dziA00 A:1-81 Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeee....eeeeee....hhhhhhhhhhhhh.......eeee..ee.....hhhhhh.......eee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------UBIQUITIN_2  PDB: A:8-79 UniProt: 1-72                                  -- PROSITE (1)
                PROSITE (2) ---------------------------------UBIQUITIN_1  PDB: A:34-59 ---------------------- PROSITE (2)
           Transcript 1 (1) -------Exon 1.1a       Exon 1.2a  PDB: A:24-59             ---------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------Exon 1.2e  PDB: A:59-81 Transcript 1 (2)
                  2dzi A  1 GSSGSSGMQLTVKALQGRECSLQVPEDELVSTLKQLVSEKLNVPVRQQRLLFKGKALADGKRLSDYSIGPNSKLNLVVKPL 81
                                    10        20        30        40        50        60        70        80

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 '\|'

NMR Structure

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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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)

Human (Homo sapiens) [TaxId: 9606] (39)

d2dzia_

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

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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)

Human (Homo sapiens) (177)

2dziA00

A:1-81

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

NMR Structure(hide GO term definitions)

Chain A (UBL4A_HUMAN | P11441)

molecular function
	GO:0051087	chaperone binding	Interacting selectively and non-covalently with a chaperone protein, a class of proteins that bind to nascent or unfolded polypeptides and ensure correct folding or transport.
	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:0019787	ubiquitin-like protein transferase activity	Catalysis of the transfer of a ubiquitin-like from one protein to another via the reaction X-ULP + Y --> Y-ULP + X, where both X-ULP and Y-ULP are covalent linkages. ULP represents a ubiquitin-like protein.
biological process
	GO:0006464	cellular protein modification process	The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
	GO:0071816	tail-anchored membrane protein insertion into ER membrane	A process of protein insertion into the endoplasmic reticulum (ER) membrane in which a tail-anchored (TA) transmembrane protein is incorporated into an endoplasmic reticulum (ER) membrane. TA transmembrane protein, also named type II transmembrane proteins, contain a single C- terminal transmembrane region.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0071818	BAT3 complex	A protein complex consisting of BAT3 (BAG6) and its cofactors. In mammals these cofactors are TRC35 (GET4) and UBL4A. It facilitates tail-anchored protein capture by ASNA1/TRC4 and also chaperones polypeptides from the endoplasmic reticulum retrotranslocation machinery to the proteasome, maintaining the solubility of substrates to improve ER-associated protein degradation (ERAD).
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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.

NMR Structure
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