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Description

Title :   SOLUTION STRUCTURE OF THE FIRST UBA DOMAIN IN THE HUMAN UBIQUITIN ASSOCIATED DOMAIN CONTAINING 1 (UBADC1)

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

Date :   14 Dec 05 (Deposition) - 14 Jun 06 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Ubiquitin Associated Domain Containing 1, Ubadc1, Uba Domain, 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, T. Kigawa, M. Sato, S. Koshiba, M. Inoue, S. Yokoyama
Solution Structure Of The First Uba Domain In The Human Ubiquitin Associated Domain Containing 1 (Ubadc1)
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Molecule 1 - UBIQUITIN ASSOCIATED DOMAIN CONTAINING 1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	CELL FREE SYNTHESIS
	Expression System Plasmid	:	P050704-09
	Expression System Vector Type	:	PLASMID
	Fragment	:	UBA DOMAIN
	Gene	:	UBADC1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS
	Synonym	:	UBADC1

Structural Features

Chains, Units


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (0, 0)

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

Sites (0, 0)

(no "Site" information available for 2DAI)

SS Bonds (0, 0)

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

Cis Peptide Bonds (0, 0)

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

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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

PROSITE Motifs (1, 1)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBA	PS50030	Ubiquitin-associated domain (UBA) profile.	UBAC1_HUMAN	187-231 288-328	1	A:23-67 -

Exons (4, 4)

NMR Structure (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000371756	1a	ENSE00001456025	chr9:138853226-138852871	356	UBAC1_HUMAN	1-46	46	0	-	-
1.2	ENST00000371756	2	ENSE00001190160	chr9:138847261-138847141	121	UBAC1_HUMAN	47-87	41	0	-	-
1.3b	ENST00000371756	3b	ENSE00000895005	chr9:138845599-138845526	74	UBAC1_HUMAN	87-111	25	0	-	-
1.4c	ENST00000371756	4c	ENSE00000895010	chr9:138839751-138839644	108	UBAC1_HUMAN	112-147	36	1	A:1-5	5
1.5	ENST00000371756	5	ENSE00000895015	chr9:138838217-138838115	103	UBAC1_HUMAN	148-182	35	1	A:6-18	13
1.6	ENST00000371756	6	ENSE00000895022	chr9:138837843-138837735	109	UBAC1_HUMAN	182-218	37	1	A:18-54	37
1.7b	ENST00000371756	7b	ENSE00000895030	chr9:138837096-138836874	223	UBAC1_HUMAN	218-292	75	1	A:54-83 (gaps)	45
1.9b	ENST00000371756	9b	ENSE00000895040	chr9:138831605-138831519	87	UBAC1_HUMAN	293-321	29	0	-	-
1.10b	ENST00000371756	10b	ENSE00000895048	chr9:138830206-138830068	139	UBAC1_HUMAN	322-368	47	0	-	-
1.11b	ENST00000371756	11b	ENSE00001456024	chr9:138825361-138824815	547	UBAC1_HUMAN	368-405	38	0	-	-

Sequences/Alignments

NMR Structure

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)
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Chain A from PDB  Type:PROTEIN  Length:83
 aligned with UBAC1_HUMAN | Q9BSL1 from UniProtKB/Swiss-Prot  Length:405

    Alignment length:124
                                   148       158       168       178       188       198       208       218       228       238       248       258    
          UBAC1_HUMAN   139 AAVQTNMRDFQTELRKILVSLIEVAQKLLALNPDAVELFKKANAMLDEDEDERVDEAALRQLTEMGFPENRATKALQLNHMSVPQAMEWLIEHAEDPTIDTPLPGQAPPEAEGATAAASEAAAG 262
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....--------------------------.......................hhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhhhh...........---------------.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------UBA  PDB: A:23-67 UniProt: 187-231           ------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4cExon 1.5  PDB: A:6-18 [INCOMPLETE] -----------------------------------Exon 1.7b  PDB: A:54-83 (gaps) [INCOMPLETE]   Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.6  PDB: A:18-54               -------------------------------------------- Transcript 1 (2)
                 2dai A   1 GSSGS--------------------------SGDAVELFKKANAMLDEDEDERVDEAALRQLTEMGFPENRATKALQLNHMSVPQAMEWLIEHAEDPTIDTPLSGPS---------------SG  83
                                |    -         -         - |      14        24        34        44        54        64        74      |  -         -  | 
                                5                          6                                                                         81              82

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Classification and Annotation

SCOP Domains (0, 0)

(no "SCOP Domain" information available for 2DAI)

CATH Domains (0, 0)

(no "CATH Domain" information available for 2DAI)

Pfam Domains (0, 0)

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

Gene Ontology (6, 6)

NMR Structure(hide GO term definitions)

Chain A (UBAC1_HUMAN | Q9BSL1)

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).
biological process
	GO:0016567	protein ubiquitination	The process in which one or more ubiquitin groups are added to a protein.
cellular component
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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