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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C2H2-TYPE ZINC FINGER DOMAIN OF HUMAN UBI-D4
 
Authors :  W. Tempel, C. Xu, C. Bian, M. Adams-Cioaba, J. Eryilmaz, C. Bountra, J. W C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, J. Min, Structural Gen Consortium (Sgc)
Date :  31 Aug 09  (Deposition) - 03 Nov 09  (Release) - 02 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics Consortium (Sgc), Zinc Finger, C2H2, Apoptosis, Metal-Binding, Nucleus, Phosphoprotein, Transcription, Transcription Regulation, Zinc-Finger, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. Zhang, C. Xu, C. Bian, W. Tempel, L. Crombet, F. Mackenzie, J. Min, Z. Liu, C. Qi
Crystal Structure Of The Cys2His2-Type Zinc Finger Domain O Human Dpf2.
Biochem. Biophys. Res. Commun. V. 413 58 2011
PubMed-ID: 21888896  |  Reference-DOI: 10.1016/J.BBRC.2011.08.043

(-) Compounds

Molecule 1 - ZINC FINGER PROTEIN UBI-D4
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28-MHL
    Expression System StrainDE3
    Expression System Taxid562
    FragmentUNP RESIDUES 203-251
    GeneDPF2, REQ, UBID4
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymREQUIEM, APOPTOSIS RESPONSE ZINC FINGER PROTEIN, D4, ZINC AND DOUBLE PHD FINGERS FAMILY 2

 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
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:211 , CYS A:214 , HIS A:227 , HIS A:232BINDING SITE FOR RESIDUE ZN A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3IUF)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3IUF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3IUF)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_FINGER_C2H2_1PS00028 Zinc finger C2H2 type domain signature.REQU_HUMAN211-232  1A:211-232

(-) Exons   (0, 0)

(no "Exon" information available for 3IUF)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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Chain A from PDB  Type:PROTEIN  Length:32
 aligned with REQU_HUMAN | Q92785 from UniProtKB/Swiss-Prot  Length:391

    Alignment length:32
                                   212       222       232  
           REQU_HUMAN   203 EDRDKPYACDICGKRYKNRPGLSYHYAHSHLA 234
               SCOP domains -------------------------------- SCOP domains
               CATH domains -------------------------------- CATH domains
               Pfam domains -------------------------------- Pfam domains
         Sec.struct. author ......ee......ee.hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------- SAPs(SNPs)
                    PROSITE --------ZINC_FINGER_C2H2_1    -- PROSITE
                 Transcript -------------------------------- Transcript
                 3iuf A 203 EDRDKPYACDICGKRYKNRPGLSYHYAHSHLA 234
                                   212       222       232  

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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3IUF)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3IUF)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3IUF)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (REQU_HUMAN | Q92785)
molecular function
    GO:0000978    RNA polymerase II core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0097190    apoptotic signaling pathway    A series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered.
    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:0005813    centrosome    A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    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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 Related Entries

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        REQU_HUMAN | Q927855b79 5vdc

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