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(-) Description

Title :  SOLUTION STRUCTURE OF THE DEAF1 MYND DOMAIN
 
Authors :  R. Spadaccini, H. Perrin, M. Bottomley, S. Ansieu, M. Sattler
Date :  08 Oct 07  (Deposition) - 25 Dec 07  (Release) - 10 Apr 13  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
NMR Structure *:  A  (1x)
Keywords :  Zinc Binding Domain, Transcription, Disease Mutation, Dna-Binding, Metal-Binding, Nucleus, Phosphorylation, Secreted, Transcription Regulation, Zinc-Finger (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Spadaccini, H. Perrin, M. J. Bottomley, S. Ansieau, M. Sattler
Retraction Notice To "Structure And Functional Analysis Of The Mynd Domain" [J. Mol. Biol. (2006) 358, 498-508].
J. Mol. Biol. V. 376 1523 2008
PubMed-ID: 18286714
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DEFORMED EPIDERMAL AUTOREGULATORY FACTOR 1 HOMOLOG
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET24D
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentMYND DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNUCLEAR DEAF-1- RELATED TRANSCRIPTIONAL REGULATOR, NUDR, SUPPRESSIN, ZINC FINGER MYND DOMAIN-CONTAINING PROTEIN 5

 Structural Features

(-) Chains, Units

  1
NMR Structure (10x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

NMR Structure (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION
NMR Structure * (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:504 , CYS A:507 , CYS A:524 , CYS A:528BINDING SITE FOR RESIDUE ZN A 601
2AC2SOFTWARECYS A:515 , CYS A:518 , HIS A:536 , CYS A:540BINDING SITE FOR RESIDUE ZN A 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2JW6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2JW6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

NMR Structure (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_013743T526NDEAF1_HUMANUnclassified  ---AT526N
2UniProtVAR_013744R530LDEAF1_HUMANUnclassified  ---AR530L
3UniProtVAR_013746Q542HDEAF1_HUMANUnclassified  ---AQ542H

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
NMR Structure * (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_013743T526NDEAF1_HUMANUnclassified  ---AT526N
2UniProtVAR_013744R530LDEAF1_HUMANUnclassified  ---AR530L
3UniProtVAR_013746Q542HDEAF1_HUMANUnclassified  ---AQ542H

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 1)

NMR Structure (2, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_MYND_1PS01360 Zinc finger MYND-type signature.DEAF1_HUMAN504-540  1A:504-540
2ZF_MYND_2PS50865 Zinc finger MYND-type profile.DEAF1_HUMAN504-540  1A:504-540
NMR Structure * (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_MYND_1PS01360 Zinc finger MYND-type signature.DEAF1_HUMAN504-540  1A:504-540
2ZF_MYND_2PS50865 Zinc finger MYND-type profile.DEAF1_HUMAN504-540  1A:504-540

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3bENST000003824093bENSE00002181507chr11:695532-694759774DEAF1_HUMAN1-97970--
1.6aENST000003824096aENSE00001491985chr11:691598-69150198DEAF1_HUMAN97-129330--
1.8ENST000003824098ENSE00001256889chr11:688460-688331130DEAF1_HUMAN130-173440--
1.9bENST000003824099bENSE00001256883chr11:688057-687911147DEAF1_HUMAN173-222500--
1.10eENST0000038240910eENSE00001378328chr11:686997-686858140DEAF1_HUMAN222-268470--
1.11bENST0000038240911bENSE00001256870chr11:684963-68489866DEAF1_HUMAN269-290220--
1.12aENST0000038240912aENSE00001256863chr11:681089-680963127DEAF1_HUMAN291-333430--
1.14ENST0000038240914ENSE00001256858chr11:679816-679688129DEAF1_HUMAN333-376440--
1.15aENST0000038240915aENSE00001256849chr11:678822-678694129DEAF1_HUMAN376-419440--
1.16aENST0000038240916aENSE00001256840chr11:674783-674536248DEAF1_HUMAN419-501830--
1.17aENST0000038240917aENSE00001256831chr11:654051-65396290DEAF1_HUMAN502-531301A:503-53129
1.20bENST0000038240920bENSE00002183525chr11:644654-644233422DEAF1_HUMAN532-565341A:532-54413

(-) 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:42
 aligned with DEAF1_HUMAN | O75398 from UniProtKB/Swiss-Prot  Length:565

    Alignment length:42
                                   512       522       532       542  
          DEAF1_HUMAN   503 SCVNCGREAMSECTGCHKVNYCSTFCQRKDWKDHQHICGQSA 544
               SCOP domains d2jw6a_ A:                                 SCOP domains
               CATH domains ------------------------------------------ CATH domains
               Pfam domains -zf-MYND-2jw6A01 A:504-540            ---- Pfam domains
         Sec.struct. author ..........ee.......ee.hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -----------------------N---L-----------H-- SAPs(SNPs)
                PROSITE (1) -ZF_MYND_2  PDB: A:504-540            ---- PROSITE (1)
                PROSITE (2) -ZF_MYND_1  PDB: A:504-540            ---- PROSITE (2)
               Transcript 1 Exon 1.17a  PDB: A:503-531   Exon 1.20b    Transcript 1
                 2jw6 A 503 SCVNCGREAMSECTGCHKVNYCSTFCQRKDWKDHQHICGQSA 544
                                   512       522       532       542  

   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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2JW6)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: TRASH (61)

(-) Gene Ontology  (25, 25)

NMR Structure(hide GO term definitions)
Chain A   (DEAF1_HUMAN | O75398)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0009653    anatomical structure morphogenesis    The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form.
    GO:0001662    behavioral fear response    An acute behavioral change resulting from a perceived external threat.
    GO:0048706    embryonic skeletal system development    The process, occurring during the embryonic phase, whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure.
    GO:0007281    germ cell development    The process whose specific outcome is the progression of an immature germ cell over time, from its formation to the mature structure (gamete). A germ cell is any reproductive cell in a multicellular organism.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    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:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0033599    regulation of mammary gland epithelial cell proliferation    Any process that modulates the frequency, rate or extent of mammary gland epithelial cell proliferation.
    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:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0008542    visual learning    Any process in an organism in which a change in behavior of an individual occurs in response to repeated exposure to a visual cue.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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.
    GO:0005667    transcription factor complex    A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

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 Related Entries

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        DEAF1_HUMAN | O753984a24 5uww

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