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(-) Description

Title :  RADR (ZIF268 VARIANT) ZINC FINGER-DNA COMPLEX (GCGT SITE)
 
Authors :  M. Elrod-Erickson, T. E. Benson, C. O. Pabo
Date :  10 Dec 97  (Deposition) - 17 Jun 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Zinc Finger-Dna Complex, Zinc Finger, Dna-Binding Protein, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Elrod-Erickson, T. E. Benson, C. O. Pabo
High-Resolution Structures Of Variant Zif268-Dna Complexes: Implications For Understanding Zinc Finger-Dna Recognition.
Structure V. 6 451 1998
PubMed-ID: 9562555  |  Reference-DOI: 10.1016/S0969-2126(98)00047-1
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*CP*GP*T)-3')
    ChainsB
    EngineeredYES
    SyntheticYES
 
Molecule 2 - DNA (5'-D(*TP*AP*CP*GP*CP*CP*CP*AP*CP*GP*C)-3')
    ChainsC
    EngineeredYES
    SyntheticYES
 
Molecule 3 - PROTEIN (RADR ZIF268 ZINC FINGER PEPTIDE)
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPRADR
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    FragmentZINC FINGER
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymRADR ZIF268 ZINC FINGER PEPTIDE

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1ZN3Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:107 , CYS A:112 , HIS A:125 , HIS A:129BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWARECYS A:137 , CYS A:140 , HIS A:153 , HIS A:157BINDING SITE FOR RESIDUE ZN A 202
3AC3SOFTWARECYS A:165 , CYS A:168 , HIS A:181 , HIS A:185BINDING SITE FOR RESIDUE ZN A 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1A1J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1A1J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1A1J)

(-) PROSITE Motifs  (1, 3)

Asymmetric/Biological Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_FINGER_C2H2_1PS00028 Zinc finger C2H2 type domain signature.EGR1_MOUSE338-360
368-388
396-416
  3A:107-129
A:137-157
A:165-185

(-) Exons   (0, 0)

(no "Exon" information available for 1A1J)

(-) 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:84
 aligned with EGR1_MOUSE | P08046 from UniProtKB/Swiss-Prot  Length:533

    Alignment length:84
                                   343       353       363       373       383       393       403       413    
           EGR1_MOUSE   334 RPYACPVESCDRRFSRSDELTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHIRTHTGEKPFACDICGRKFARSDERKRHTKIHL 417
               SCOP domains d1a1ja1 A:103-131 ZIF268     d1a1ja2 A:132-159 ZIF268    d1a1ja3 A:160-186 ZIF268    SCOP domains
               CATH domains 1a1jA01 A:103-132             1a1jA02 A:133-159          1a1jA03 A:160-186           CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee........ee..hhhhhhhhhhhh....ee......ee..hhhhhhhhhhhh....ee......ee..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----ZINC_FINGER_C2H2_1     -------ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1   - PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                 1a1j A 103 RPYACPVESCDRRFSRSADLTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHIRTHTGEKPFACDICGRKFARSDERKRHTKIHL 186
                                   112       122       132       142       152       162       172       182    

Chain B from PDB  Type:DNA  Length:11
                                           
                 1a1j B   1 AGCGTGGGCGT  11
                                    10 

Chain C from PDB  Type:DNA  Length:11
                                           
                 1a1j C  51 TACGCCCACGC  61
                                    60 

   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, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1A1J)

(-) Gene Ontology  (36, 36)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (EGR1_MOUSE | P08046)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003700    DNA-binding transcription factor activity    A protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a gene to modulate transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
    GO:0000977    RNA polymerase II regulatory region sequence-specific DNA binding    Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
    GO:0035035    histone acetyltransferase binding    Interacting selectively and non-covalently with the enzyme histone acetyltransferase.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0001077    proximal promoter DNA-binding transcription activator activity, RNA polymerase II-specific    A protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within a proximal promoter regulatory region of a RNA polymerase II-transcribed gene to activate or increase transcription.
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0000982    transcription factor activity, RNA polymerase II proximal promoter 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 (RNAP II) in order to modulate transcription by RNAP II.
    GO:0044212    transcription regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
    GO:0000976    transcription regulatory region sequence-specific DNA binding    Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon.
biological process
    GO:0030509    BMP signaling pathway    A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0030217    T cell differentiation    The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex.
    GO:0071480    cellular response to gamma radiation    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 gamma radiation stimulus. Gamma radiation is a form of electromagnetic radiation (EMR) or light emission of a specific frequency produced from sub-atomic particle interaction, such as electron-positron annihilation and radioactive decay. Gamma rays are generally characterized as EMR having the highest frequency and energy, and also the shortest wavelength, within the electromagnetic radiation spectrum.
    GO:0071504    cellular response to heparin    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 heparin stimulus.
    GO:0071506    cellular response to mycophenolic 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 mycophenolic acid stimulus.
    GO:0071310    cellular response to organic substance    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 an organic substance stimulus.
    GO:0072110    glomerular mesangial cell proliferation    The multiplication or reproduction of glomerular mesangial cells, resulting in the expansion of the population.
    GO:0070498    interleukin-1-mediated signaling pathway    A series of molecular signals initiated by the binding of interleukin-1 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0090090    negative regulation of canonical Wnt signaling pathway    Any process that decreases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
    GO:0000122    negative regulation of transcription by RNA polymerase II    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription mediated by RNA polymerase II.
    GO:0072303    positive regulation of glomerular metanephric mesangial cell proliferation    Any process that increases the frequency, rate or extent of metanephric glomerular mesangial cell proliferation.
    GO:0045944    positive regulation of transcription by RNA polymerase II    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    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:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:0033233    regulation of protein sumoylation    Any process that modulates the frequency, rate or extent of the addition of SUMO groups to a protein.
    GO:0061418    regulation of transcription from RNA polymerase II promoter in response to hypoxia    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a hypoxia stimulus.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0009749    response to glucose    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucose stimulus.
    GO:0032868    response to insulin    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
    GO:0035914    skeletal muscle cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a skeletal muscle cell, a somatic cell located in skeletal muscle.
    GO:0006366    transcription by RNA polymerase II    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        EGR1_MOUSE | P080461a1f 1a1g 1a1h 1a1i 1a1k 1a1l 1aay 1f2i 1g2d 1g2f 1jk1 1jk2 1llm 1p47 1zaa

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1A1J)