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(-) Description

Title :  SOLUTION STRUCTURE OF THE HMG BOX DOMAIN FROM HUMAN WD REPEAT AND HMG-BOX DNA BINDING PROTEIN 1
 
Authors :  T. Tomizawa, T. Kigawa, K. Saito, S. Koshiba, M. Inoue, Y. O. Kamatari, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  24 Nov 05  (Deposition) - 24 May 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  High Mobility Group Box Domain, Helix-Turn-Helix, Dna Binding, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Gene Regulation, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Tomizawa, T. Kigawa, K. Saito, S. Koshiba, M. Inoue, Y. O. Kamatari, S. Yokoyama
Solution Structure Of The Hmg Box Domain From Human Wd Repeat And Hmg-Box Dna Binding Protein 1
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - WD REPEAT AND HMG-BOX DNA BINDING PROTEIN 1
    Chains: A
    Engineered: YES
    Expression System Plasmid: P050111-08
    Expression System Vector Type: PLASMID
    Fragment: HMG BOX DOMAIN
    Gene: WDHD1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CELL-FREE PROTEIN SYNTHESIS
    Synonym: ACIDIC NUCLEOPLASMIC DNA- BINDING PROTEIN 1, AND- 1

 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 2D7L)

(-) Sites  (0, 0)

(no "Site" information available for 2D7L)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2D7L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2D7L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D7L)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HMG_BOX_2PS50118 HMG boxes A and B DNA-binding domains profile.WDHD1_HUMAN1015-1084  1A:8-75

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000003605861cENSE00001890909chr14:55493795-5549374650WDHD1_HUMAN-00--
1.1eENST000003605861eENSE00002195219chr14:55493521-5549342993WDHD1_HUMAN1-26260--
1.2ENST000003605862ENSE00001606792chr14:55480314-55480203112WDHD1_HUMAN26-63380--
1.3ENST000003605863ENSE00001770131chr14:55477178-55477027152WDHD1_HUMAN64-114510--
1.4ENST000003605864ENSE00001740647chr14:55475437-55475326112WDHD1_HUMAN114-151380--
1.5ENST000003605865ENSE00002157060chr14:55475084-5547503451WDHD1_HUMAN152-168170--
1.6ENST000003605866ENSE00000572360chr14:55474093-5547399896WDHD1_HUMAN169-200320--
1.7ENST000003605867ENSE00000657700chr14:55468903-5546881193WDHD1_HUMAN201-231310--
1.8ENST000003605868ENSE00002152866chr14:55467710-55467604107WDHD1_HUMAN232-267360--
1.9ENST000003605869ENSE00000657696chr14:55467362-55467221142WDHD1_HUMAN267-314480--
1.10ENST0000036058610ENSE00000657694chr14:55462531-55462321211WDHD1_HUMAN315-385710--
1.11ENST0000036058611ENSE00000657692chr14:55458118-55457931188WDHD1_HUMAN385-447630--
1.12ENST0000036058612ENSE00000657691chr14:55455930-55455746185WDHD1_HUMAN448-509620--
1.13ENST0000036058613ENSE00000657689chr14:55454105-55453864242WDHD1_HUMAN509-590820--
1.14ENST0000036058614ENSE00001388096chr14:55451578-55451441138WDHD1_HUMAN590-636470--
1.15ENST0000036058615ENSE00000657685chr14:55448414-55448258157WDHD1_HUMAN636-688530--
1.16ENST0000036058616ENSE00000657683chr14:55434112-55433998115WDHD1_HUMAN688-726390--
1.17ENST0000036058617ENSE00000657681chr14:55433324-55433193132WDHD1_HUMAN727-770440--
1.18ENST0000036058618ENSE00000657679chr14:55429890-55429670221WDHD1_HUMAN771-844740--
1.19ENST0000036058619ENSE00000657677chr14:55429571-55429456116WDHD1_HUMAN844-883400--
1.20ENST0000036058620ENSE00000657675chr14:55429269-5542921654WDHD1_HUMAN883-901190--
1.21ENST0000036058621ENSE00000657673chr14:55424353-5542431044WDHD1_HUMAN901-915150--
1.22ENST0000036058622ENSE00000657671chr14:55423922-55423752171WDHD1_HUMAN916-972570--
1.23ENST0000036058623ENSE00000657669chr14:55422412-55422279134WDHD1_HUMAN973-1017451A:1-8 (gaps)45
1.24bENST0000036058624bENSE00000657667chr14:55411188-55411050139WDHD1_HUMAN1017-1063471A:8-5447
1.25dENST0000036058625dENSE00001907538chr14:55408408-554056682741WDHD1_HUMAN1064-1129661A:55-81 (gaps)32

(-) 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:81
 aligned with WDHD1_HUMAN | O75717 from UniProtKB/Swiss-Prot  Length:1129

    Alignment length:123
                                   982       992      1002      1012      1022      1032      1042      1052      1062      1072      1082      1092   
         WDHD1_HUMAN    973 ASAASYFQKRNSQTNKTEEVKEENLKNVLSETPAICPPQNTENQRPKTGFQMWLEENRSNILSDNPDFSDEADIIKEGMIRFRVLSTEERKVWANKAKGETASEGTEAKKRKRVVDESDETEN 1095
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....-------------------------------------.....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhhhhhhhh..........hhhhh-----...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------HMG_BOX_2  PDB: A:8-75 UniProt: 1015-1084                             ----------- PROSITE
           Transcript 1 (1) Exon 1.23  PDB: A:1-8 (gaps)                 ----------------------------------------------Exon 1.25d  PDB: A:55-81 (gaps)  Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------Exon 1.24b  PDB: A:8-54 UniProt: 1017-1063     -------------------------------- Transcript 1 (2)
                2d7l A    1 GSSGS-------------------------------------SGRPKTGFQMWLEENRSNILSDNPDFSDEADIIKEGMIRFRVLSTEERKVWANKAKGETASEGTEAKKRK-----SGPSSG   81
                                |    -         -         -         -  |     13        23        33        43        53        63        73 |     |78   
                                5                                     6                                                                   75    76
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (0, 0)

(no "SCOP Domain" information available for 2D7L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2D7L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D7L)

(-) Gene Ontology  (5, 5)

NMR Structure(hide GO term definitions)
Chain A   (WDHD1_HUMAN | O75717)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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).
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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

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UniProtKB/Swiss-Prot
        WDHD1_HUMAN | O75717: 5gva 5gvb

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