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(-) Description

Title :  SOLUTION STRUCTURE OF THE SWIB DOMAIN OF MOUSE BRG1-ASSOCIATED FACTOR 60A
 
Authors :  K. Yamada, K. Saito, N. Nameki, M. Inoue, S. Koshiba, M. Shirouzu, T. Terada, T. Yabuki, M. Aoki, T. Matsuda, E. Seki, H. Hirota, M. Yoshida, A. Tanaka, T. Osanai, T. Arakawa, P. Carninci, J. Kawai, Y. Hayashizaki, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  09 Jul 03  (Deposition) - 24 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Structural Genomics, Swi/Snf, Chromatin Remodeling, Riken Structural Genomics/Proteomics Initiative, Rsgi, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Yamada, K. Saito, N. Nameki, M. Inoue, S. Koshiba, M. Shirouzu, T. Terada, T. Yabuki, M. Aoki, T. Matsuda, E. Seki, H. Hirota, M. Yoshida, A. Tanaka, T. Osanai, T. Arakawa, P. Carninci, J. Kawai, Y. Hayashizaki, T. Kigawa, S. Yokoyama
Solution Structure Of The Swib Domain Of Mouse Brg1-Associated Factor 60A
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SWI/SNF RELATED, MATRIX ASSOCIATED, ACTIN DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY D MEMBER 1
    Chains: A
    Engineered: YES
    Expression System Plasmid: P020826-29
    Expression System Vector Type: PLASMID
    Fragment: SWIB DOMAIN
    Gene: RIKEN CDNA 0710008A09
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: CELL-FREE PROTEIN SYNTHESIS
    Synonym: BRG1-ASSOCIATED FACTOR 60A, BAF60A

 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 1UHR)

(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

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(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) 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
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Chain A from PDB  Type:PROTEIN  Length:93
 aligned with SMRD1_MOUSE | Q61466 from UniProtKB/Swiss-Prot  Length:515

    Alignment length:122
                                   272       282       292       302       312       322       332       342       352       362       372       382  
          SMRD1_MOUSE   263 TTQETDGFQVKRPGDVNVRCTVLLMLDYQPPQFKLDPRLARLLGIHTQTRPVIIQALWQYIKTHKLQDPHEREFVLCDKYLQQIFESQRMKFSEIPQRLHALLMPPEPIIINHVISVDPNDQ 384
               SCOP domains d1uhra_                      A: SWI/SNF related regulator of chromatin (BRG1-associated factor 60a)                        SCOP domains
               CATH domains 1uhrA00                      A:1-93 MDM2                                                                                   CATH domains
               Pfam domains ----------------------------SWIB-1uhrA01 A:8-83                                                         ------------------ Pfam domains
         Sec.struct. author .......---------------------....eee..hhhhhh...ee.hhhhhhhhhhhhhhh.........eee...hhhhhh...eee...hhhhhhhhee....--------...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uhr A   1 GSSGSSG---------------------QPPQFKLDPRLARLLGIHTQTRPVIIQALWQYIKTHKLQDPHEREFVLCDKYLQQIFESQRMKFSEIPQRLHALLMPPEP--------SGPSSG  93
                                  |  -         -        |9        19        29        39        49        59        69        79       | -      | 91  
                                  7                     8                                                                             87       88
   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: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: SWIB] (22)

(-) Gene Ontology  (14, 14)

NMR Structure(hide GO term definitions)
Chain A   (SMRD1_MOUSE | Q61466)
molecular function
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    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:0032947    protein complex scaffold activity    A structural molecule activity that provides a physical support for the assembly of a multiprotein complex. The scaffold may or may not be part of the final complex.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
    GO:0071398    cellular response to fatty acid    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a fatty acid stimulus.
    GO:0006338    chromatin remodeling    Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
    GO:0048096    chromatin-mediated maintenance of transcription    Maintenance of transcription by remodelling of chromatin into an 'open configuration'. Once established, this regulation is mitotically stable and is maintained over many cell divisions. It is also heritable.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0006337    nucleosome disassembly    The controlled breakdown of nucleosomes, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
cellular component
    GO:0090544    BAF-type complex    A SWI/SNF-type complex that contains a subunit from the BAF (Brahma-Associated Factor) family.
    GO:0016514    SWI/SNF complex    A SWI/SNF-type complex that contains nine or more proteins, including both conserved (core) and nonconserved components; the Swi2/Snf2 ATPase is one of the core components.
    GO:0071565    nBAF complex    A SWI/SNF-type complex that is found in post-mitotic neurons, and in human contains actin and proteins encoded by the ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, DPF1/BAF45B, DPF3/BAF45C, ACTL6B/BAF53B genes. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth.
    GO:0071564    npBAF complex    A SWI/SNF-type complex that is found in neural stem or progenitor cells, and in human contains actin and proteins encoded by the ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, PHF10/BAF45A, ACTL6A/BAF53A genes. The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells.
    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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