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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HBAF250B AT-RICH INTERACTION DOMAIN (ARID)
 
Authors :  A. Shimada, H. Niwa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  01 Jul 05  (Deposition) - 10 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Dna-Binding Domain, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Shimada, H. Niwa, S. Yokoyama
Crystal Structure Of The Hbaf250B At-Rich Interaction Domain (Arid)
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BAF250B SUBUNIT
    Chains: A
    Engineered: YES
    Expression System: CELL FREE SYNTHESIS
    Expression System Plasmid: PX041105-20
    Expression System Vector Type: PLASMID
    Fragment: AT-RICH INTERACTION DOMAIN (ARID)
    Gene: HBAF250B
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CELL-FREE PROTEIN SYNTHESIS
    Synonym: HBAF250B

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1MSE1Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2CXY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_067678V1092IARI1B_HUMANPolymorphism775526039AV52I
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ARIDPS51011 ARID domain profile.ARI1B_HUMAN1053-1144  1A:13-104

(-) Exons   (2, 2)

Asymmetric/Biological Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003500261aENSE00002076297chr6:157099063-1571006051543ARI1B_HUMAN1-5145140--
1.2ENST000003500262ENSE00002193707chr6:157150361-157150555195ARI1B_HUMAN515-579650--
1.5bENST000003500265bENSE00002196548chr6:157222510-157222659150ARI1B_HUMAN580-629500--
1.6aENST000003500266aENSE00001744727chr6:157256600-157256710111ARI1B_HUMAN630-666370--
1.7aENST000003500267aENSE00002178237chr6:157405796-157406039244ARI1B_HUMAN667-748820--
1.8aENST000003500268aENSE00002147736chr6:157431606-15743169590ARI1B_HUMAN748-778310--
1.9aENST000003500269aENSE00000765473chr6:157454162-157454341180ARI1B_HUMAN778-838610--
1.10aENST0000035002610aENSE00001332230chr6:157469758-157470085328ARI1B_HUMAN838-9471100--
1.11ENST0000035002611ENSE00002140579chr6:157488174-157488319146ARI1B_HUMAN947-996500--
1.12ENST0000035002612ENSE00002197298chr6:157495142-157495251110ARI1B_HUMAN996-1032370--
1.14aENST0000035002614aENSE00001696442chr6:157502103-157502312210ARI1B_HUMAN1033-1102701A:1-6262
1.15aENST0000035002615aENSE00000975824chr6:157505365-157505569205ARI1B_HUMAN1103-1171691A:63-11452
1.16ENST0000035002616ENSE00001142078chr6:157510776-157510914139ARI1B_HUMAN1171-1217470--
1.17ENST0000035002617ENSE00001142072chr6:157511172-157511344173ARI1B_HUMAN1217-1275590--
1.18ENST0000035002618ENSE00001142064chr6:157517299-157517449151ARI1B_HUMAN1275-1325510--
1.19ENST0000035002619ENSE00001142057chr6:157519945-15752004197ARI1B_HUMAN1325-1357330--
1.20aENST0000035002620aENSE00000975829chr6:157521839-157522622784ARI1B_HUMAN1358-16192620--
1.21ENST0000035002621ENSE00001142049chr6:157525000-157525130131ARI1B_HUMAN1619-1662440--
1.22cENST0000035002622cENSE00002020018chr6:157527301-1575302842984ARI1B_HUMAN1663-22365740--

(-) Sequences/Alignments

Asymmetric/Biological Unit
   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:114
 aligned with ARI1B_HUMAN | Q8NFD5 from UniProtKB/Swiss-Prot  Length:2236

    Alignment length:114
                                  1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150    
         ARI1B_HUMAN   1041 GEKITKVYELGNEPERKLWVDRYLTFMEERGSPVSSLPAVGKKPLDLFRLYVCVKEIGGLAQVNKNKKWRELATNLNVGTSSSAASSLKKQYIQYLFAFECKIERGEEPPPEVF 1154
               SCOP domains d2cxya_ A: automated matches                                                                                       SCOP domains
               CATH domains 2cxyA00 A:1-114  [code=1.10.150.60, no name defined]                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhh....hhhhhhhhhhhhhhhhh.......ee..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------I-------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------ARID  PDB: A:13-104 UniProt: 1053-1144                                                      ---------- PROSITE
               Transcript 1 Exon 1.14a  PDB: A:1-62 UniProt: 1033-1102 [INCOMPLETE]       Exon 1.15a  PDB: A:63-114 UniProt: 1103-1171         Transcript 1
                2cxy A    1 GEKITKVYELGNEPERKLWVDRYLTFmEERGSPVSSLPAVGKKPLDLFRLYVCVKEIGGLAQVNKNKKWRELATNLNVGTSSSAASSLKKQYIQYLFAFECKIERGEEPPPEVF  114
                                    10        20      | 30        40        50        60        70        80        90       100       110    
                                                     27-MSE
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ARI1B_HUMAN | Q8NFD5)
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).
    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: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:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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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        ARI1B_HUMAN | Q8NFD5: 2eh9

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