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(-) Description

Title :  SOLUTION STRUCTURE OF THE UBX DOMAIN OF KIAA0794 PROTEIN
 
Authors :  H. Zhang, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  28 May 04  (Deposition) - 28 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Ubx Domain, Beta-Grasp Fold, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Zhang, F. Hayashi, S. Yokoyama
Solution Structure Of The Ubx Domain Of Kiaa0794 Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - KIAA0794 PROTEIN
    Chains: A
    Engineered: YES
    Expression System Plasmid: P040114-84
    Expression System Vector Type: PLASMID
    Fragment: UBX DOMAIN
    Gene: KAZUSA CDNA HK06006
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CELL FREE PROTEIN SYNTHESIS

 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 1WJ4)

(-) Sites  (0, 0)

(no "Site" information available for 1WJ4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WJ4)

(-) Cis Peptide Bonds  (2, 40)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Phe A:89 -Pro A:90
21, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Cys A:109 -Pro A:110

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WJ4)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBXPS50033 UBX domain profile.UBXN7_HUMAN408-485  1A:39-116

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002963281aENSE00001290985chr3:196159345-196159198148UBXN7_HUMAN1-25250--
1.4ENST000002963284ENSE00001670290chr3:196134264-196134117148UBXN7_HUMAN25-74500--
1.5ENST000002963285ENSE00001595418chr3:196129890-19612982368UBXN7_HUMAN74-97240--
1.7bENST000002963287bENSE00001741987chr3:196120490-19612042566UBXN7_HUMAN97-119230--
1.8bENST000002963288bENSE00001774298chr3:196118796-196118684113UBXN7_HUMAN119-156380--
1.9ENST000002963289ENSE00001677336chr3:196098913-196098767147UBXN7_HUMAN157-205490--
1.10ENST0000029632810ENSE00001606845chr3:196096382-19609629291UBXN7_HUMAN206-236310--
1.11ENST0000029632811ENSE00001750602chr3:196095026-196094899128UBXN7_HUMAN236-278430--
1.12ENST0000029632812ENSE00001611820chr3:196089558-196089165394UBXN7_HUMAN279-4101321A:1-41 (gaps)86
1.13ENST0000029632813ENSE00001718795chr3:196088794-19608871580UBXN7_HUMAN410-436271A:41-6727
1.14cENST0000029632814cENSE00001265446chr3:196083717-1960745339185UBXN7_HUMAN437-489531A:68-12053

(-) 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)
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:124
 aligned with UBXN7_HUMAN | O94888 from UniProtKB/Swiss-Prot  Length:489

    Alignment length:169
                                                                                                                                                                                              489    
                                   334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484    |    
          UBXN7_HUMAN   325 GSEEFISVCGSDEEEEVENLAKSRKSPHKDLGHRKEENRRPLTEPPVRTDPGTATNHQGLPAVDSEILEMPPEKADGVVEGIDVNGPKAQLMLRYPDGKREQITLPEQAKLLALVKHVQSKGYPNERFELLTNFPRRKLSHLDYDITLQEAGLCPQETVFVQERN----   -
               SCOP domains d1      wj4a                                       _ A: Hypothetical protein KIAA0794                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------UBX-1wj4A01 A:38-118                                                             ------ Pfam domains
         Sec.struct. author ..------....---------------------------------------.....................................eeeeeee...eeeeeee....hhhhhhhhhhhhhh....eeeee....eee................eeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------UBX  PDB: A:39-116 UniProt: 408-485                                           -------- PROSITE
           Transcript 1 (1) Exon 1.12  PDB: A:1-41 (gaps) UniProt: 279-410 [INCOMPLETE]                           --------------------------Exon 1.14c  PDB: A:68-120 UniProt: 437-489           ---- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------Exon 1.13  PDB: A:41-67    --------------------------------------------------------- Transcript 1 (2)
                 1wj4 A   1 GS------SGSS---------------------------------------GTATNHQGLPAVDSEILEMPPEKADGVVEGIDVNGPKAQLMLRYPDGKREQITLPEQAKLLALVKHVQSKGYPNERFELLTNFPRRKLSHLDYDITLQEAGLCPQETVFVQESGPSSG 124
                             |      |4 |       -         -         -         - |      15        25        35        45        55        65        75        85        95       105       115         
                             2      3  6                                       7
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1WJ4)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: Ubiquitin (279)

(-) Gene Ontology  (7, 7)

NMR Structure(hide GO term definitions)
Chain A   (UBXN7_HUMAN | O94888)
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:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    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.
cellular component
    GO:0034098    VCP-NPL4-UFD1 AAA ATPase complex    A multiprotein ATPase complex required for the efficient dislocation of ER-lumenal degradation substrates, and their subsequent proteolysis by the proteasome. In budding yeast, this complex includes Cdc48p, Npl4p and Ufd1p proteins. In mammals, this complex includes a hexamer of VCP/p97 (a cytosolic ATPase) and trimers of each of its cofactors UFD1L and NPL4 (NPLOC4) (e.g. a 6:3:3 stoichiometry).
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        UBXN7_HUMAN | O94888: 2dal 2dlx 5x3p 5x4l

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