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(-) Description

Title :  SOLUTION STRUCTURE OF THE SWI1 ARID
 
Authors :  S. Kim, Z. Zhang, S. Upchurch, N. Isern, Y. Chen
Date :  22 Dec 03  (Deposition) - 25 May 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (8x)
Keywords :  Arid, Swi1, Nmr, Structural Genomics, Protein-Dna Interaction, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Kim, Z. Zhang, S. Upchurch, N. Isern, Y. Chen
Structure And Dna-Binding Sites Of The Swi1 At-Rich Interaction Domain (Arid) Suggest Determinants For Sequence-Specific Dna Recognition.
J. Biol. Chem. V. 279 16670 2004
PubMed-ID: 14722072  |  Reference-DOI: 10.1074/JBC.M312115200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SWI/SNF-RELATED, MATRIX-ASSOCIATED, ACTIN- DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY F MEMBER 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Strain: BL21DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: SWI1 ARID (RESIDUES 617-736)
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SWI-SNF COMPLEX PROTEIN P270, B120

 Structural Features

(-) Chains, Units

  
NMR Structure (8x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1RYU)

(-) Sites  (0, 0)

(no "Site" information available for 1RYU)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1RYU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_064695R1020KARI1A_HUMANUnclassified  ---AR21K
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ARIDPS51011 ARID domain profile.ARI1A_HUMAN1017-1108  1A:18-109

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003248561aENSE00001907429chr1:27022524-270240311508ARI1A_HUMAN1-3793790--
1.3bENST000003248563bENSE00001349776chr1:27056142-27056354213ARI1A_HUMAN380-450710--
1.4bENST000003248564bENSE00000902180chr1:27057643-27058095453ARI1A_HUMAN451-6011510--
1.5ENST000003248565ENSE00001227857chr1:27059167-27059283117ARI1A_HUMAN602-640390--
1.6ENST000003248566ENSE00001349762chr1:27087347-27087587241ARI1A_HUMAN641-721810--
1.7ENST000003248567ENSE00001349761chr1:27087875-2708796490ARI1A_HUMAN721-751310--
1.8ENST000003248568ENSE00001349760chr1:27088643-27088810168ARI1A_HUMAN751-807570--
1.9ENST000003248569ENSE00001157462chr1:27089464-27089776313ARI1A_HUMAN807-9111050--
1.10aENST0000032485610aENSE00000761096chr1:27092712-27092857146ARI1A_HUMAN911-960500--
1.10cENST0000032485610cENSE00001349753chr1:27092948-27093057110ARI1A_HUMAN960-996370--
1.11aENST0000032485611aENSE00001349752chr1:27094281-27094490210ARI1A_HUMAN997-1066701A:1-6767
1.12aENST0000032485612aENSE00000872621chr1:27097610-27097817208ARI1A_HUMAN1067-1136701A:68-12053
1.13ENST0000032485613ENSE00001227772chr1:27098991-27099123133ARI1A_HUMAN1136-1180450--
1.14aENST0000032485614aENSE00001227767chr1:27099303-27099478176ARI1A_HUMAN1180-1239600--
1.15ENST0000032485615ENSE00001227760chr1:27099837-27099987151ARI1A_HUMAN1239-1289510--
1.16ENST0000032485616ENSE00000761089chr1:27100071-27100208138ARI1A_HUMAN1289-1335470--
1.17ENST0000032485617ENSE00001349740chr1:27100293-2710038997ARI1A_HUMAN1335-1367330--
1.18aENST0000032485618aENSE00001349739chr1:27100820-27101711892ARI1A_HUMAN1368-16652980--
1.19ENST0000032485619ENSE00000872637chr1:27102068-27102198131ARI1A_HUMAN1665-1708440--
1.21fENST0000032485621fENSE00001883917chr1:27105514-271085953082ARI1A_HUMAN1709-22855770--

(-) 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:120
 aligned with ARI1A_HUMAN | O14497 from UniProtKB/Swiss-Prot  Length:2285

    Alignment length:120
                                  1009      1019      1029      1039      1049      1059      1069      1079      1089      1099      1109      1119
         ARI1A_HUMAN   1000 SSTTTNEKITKLYELGGEPERKMWVDRYLAFTEEKAMGMTNLPAVGRKPLDLYRLYVSVKEIGGLTQVNKNKKWRELATNLNVGTSSSAASSLKKQYIQCLYAFECKIERGEDPPPDIFA 1119
               SCOP domains d1ryua_ A: SWI-SNF complex protein p270, SMARCF1                                                                         SCOP domains
               CATH domains 1ryuA00 A:1-120  [code=1.10.150.60, no name defined]                                                                     CATH domains
               Pfam domains ---------------ARID-1ryuA01 A:16-105                                                                     --------------- Pfam domains
         Sec.struct. author .........hhhhh...hhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhh..hhhhh.hhhhhhhhhh.....hhhhhhhhhhhhhhh................... Sec.struct. author
                 SAPs(SNPs) --------------------K--------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------ARID  PDB: A:18-109 UniProt: 1017-1108                                                      ----------- PROSITE
               Transcript 1 Exon 1.11a  PDB: A:1-67 UniProt: 997-1066 [INCOMPLETE]             Exon 1.12a  PDB: A:68-120 UniProt: 1067-1136          Transcript 1
                1ryu A    1 SSTTTNEKITKLYELGGEPERKMWVDRYLAFTEEKAMGMTNLPAVGRKPLDLYRLYVSVKEIGGLTQVNKNKKWRELATNLNVGTSSSAASSLKKQYIQCLYAFECKIERGEDPPPDIFA  120
                                    10        20        30        40        50        60        70        80        90       100       110       120
   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: ARID] (8)

(-) Gene Ontology  (35, 35)

NMR Structure(hide GO term definitions)
Chain A   (ARI1A_HUMAN | O14497)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0016922    ligand-dependent nuclear receptor binding    Interacting selectively and non-covalently, in a ligand dependent manner, with a nuclear receptor protein.
    GO:0031491    nucleosome binding    Interacting selectively and non-covalently with a nucleosome, a complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
    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:0003713    transcription coactivator activity    Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
biological process
    GO:0043044    ATP-dependent chromatin remodeling    Dynamic structural changes to eukaryotic chromatin that require energy from the hydrolysis of ATP, ranging from local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation, mediated by ATP-dependent chromatin-remodelling factors.
    GO:0030521    androgen receptor signaling pathway    Any series of molecular signals generated as a consequence of an androgen binding to its receptor.
    GO:0003205    cardiac chamber development    The progression of a cardiac chamber over time, from its formation to the mature structure. A cardiac chamber is an enclosed cavity within the heart.
    GO:0055007    cardiac muscle cell differentiation    The process in which a cardiac muscle precursor cell acquires specialized features of a cardiac muscle cell. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction.
    GO:0006325    chromatin organization    Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin.
    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:0030900    forebrain development    The process whose specific outcome is the progression of the forebrain over time, from its formation to the mature structure. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions).
    GO:0042921    glucocorticoid receptor signaling pathway    Any series of molecular signals generated as a consequence of a glucocorticoid binding to its receptor.
    GO:0030520    intracellular estrogen receptor signaling pathway    Any series of molecular signals generated as a consequence of an intracellular estrogen receptor binding to one of its physiological ligands. The pathway begins with receptor-ligand binding, and ends with regulation of a downstream cellular process (e.g. transcription).
    GO:0006344    maintenance of chromatin silencing    The maintenance of chromatin in a transcriptionally silent state such as heterochromatin.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    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:0001843    neural tube closure    The last step in the formation of the neural tube, where the paired neural folds are brought together and fuse at the dorsal midline.
    GO:0006337    nucleosome disassembly    The controlled breakdown of nucleosomes, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
    GO:0042766    nucleosome mobilization    The movement of nucleosomes along a DNA fragment.
    GO:0003408    optic cup formation involved in camera-type eye development    The developmental process pertaining to the initial formation of the optic cup, a two-walled vesicle formed from the optic vesicle.
    GO:0060674    placenta blood vessel development    The process whose specific outcome is the progression of a blood vessel of the placenta over time, from its formation to the mature structure.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:1901998    toxin transport    The directed movement of a toxin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of 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:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    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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