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(-) Description

Title :  GFI-1 ZINC FINGERS 3-5 COMPLEXED WITH DNA
 
Authors :  S. Lee, Z. Wu
Date :  30 Jul 09  (Deposition) - 02 Mar 10  (Release) - 26 May 10  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C  (12x)
Keywords :  Tandem Repeat Zinc Finger Domain, Protein-Dna Complex, Dna-Binding, Metal-Binding, Nucleus, Transcription, Transcription Regulation, Zinc, Zinc-Finger, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Lee, K. Doddapaneni, A. Hogue, L. Mcghee, S. Meyers, Z. Wu
Solution Structure Of Gfi-1 Zinc Domain Bound To Consensus Dna.
J. Mol. Biol. V. 397 1055 2010
PubMed-ID: 20153336  |  Reference-DOI: 10.1016/J.JMB.2010.02.006

(-) Compounds

Molecule 1 - ZINC FINGER PROTEIN GFI-1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3) PLYSS
    Expression System Taxid562
    Expression System VectorPET17B
    FragmentUNP RESIDUES 312-393
    GeneGFI1, GFI-1
    Organism CommonBROWN RAT,RAT,RATS
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymGROWTH FACTOR INDEPENDENT PROTEIN 1
 
Molecule 2 - DNA (5'-D(*CP*AP*TP*AP*AP*AP*TP*CP*AP*CP*TP*GP*CP*CP*TP*A)- 3')
    ChainsB
    EngineeredYES
    SyntheticYES
 
Molecule 3 - DNA (5'-D(*TP*AP*GP*GP*CP*AP*GP*TP*GP*AP*TP*TP*TP*AP*TP*G)- 3')
    ChainsC
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  
NMR Structure (12x)

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 3)
No.NameCountTypeFull Name
1ZN3Ligand/IonZINC ION

(-) Sites  (3, 3)

NMR Structure (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:4 , CYS A:7 , HIS A:20 , HIS A:24BINDING SITE FOR RESIDUE ZN A 83
2AC2SOFTWARECYS A:32 , CYS A:35 , HIS A:48 , HIS A:52BINDING SITE FOR RESIDUE ZN A 84
3AC3SOFTWARECYS A:60 , CYS A:63 , HIS A:76 , HIS A:80BINDING SITE FOR RESIDUE ZN A 85

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2KMK)

(-) PROSITE Motifs  (1, 3)

NMR Structure (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_FINGER_C2H2_1PS00028 Zinc finger C2H2 type domain signature.GFI1_RAT258-279
287-307
315-335
343-363
371-391
399-420
  3-
-
A:4-24
A:32-52
A:60-80
-

(-) Exons   (0, 0)

(no "Exon" information available for 2KMK)

(-) 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:82
 aligned with GFI1_RAT | Q07120 from UniProtKB/Swiss-Prot  Length:423

    Alignment length:82
                                   321       331       341       351       361       371       381       391  
             GFI1_RAT   312 SFDCKICGKSFKRSSTLSTHLLIHSDTRPYPCQYCGKRFHQKSDMKKHTFIHTGEKPHKCQVCGKAFSQSSNLITHSRKHTG 393
               SCOP domains d2kmka_ A: automated matches                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -zf-C2H2-2kmkA01 A:2-24 -----------------------------------------------zf-H2C2_2-2 Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------zf-H2C2_2-2 Pfam domains (2)
         Sec.struct. author .ee......ee.hhhhhhhhhhhhhh...ee......ee.hhhhhhhhhhhhhh...ee......ee.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1   -- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 2kmk A   1 SFDCKICGKSFKRSSTLSTHLLIHSDTRPYPCQYCGKRFHQKSDMKKHTFIHTGEKPHKCQVCGKAFSQSSNLITHSRKHTG  82
                                    10        20        30        40        50        60        70        80  

Chain B from PDB  Type:DNA  Length:16
                                                
                 2kmk B 101 CATAAATCACTGCCTA 116
                                   110      

Chain C from PDB  Type:DNA  Length:16
                                                
                 2kmk C 201 TAGGCAGTGATTTATG 216
                                   210      

   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 2KMK)

(-) Pfam Domains  (2, 3)

NMR Structure
(-)
Clan: C2H2-zf (71)

(-) Gene Ontology  (26, 26)

NMR Structure(hide GO term definitions)
Chain A   (GFI1_RAT | Q07120)
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:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic 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: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:0001078    transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific 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 stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
    GO:0071222    cellular response to lipopolysaccharide    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 lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0030097    hemopoiesis    The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates.
    GO:0030099    myeloid cell differentiation    The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte, megakaryocyte, thrombocyte, or erythrocyte lineages.
    GO:0010956    negative regulation of calcidiol 1-monooxygenase activity    Any process that decreases the rate, frequency or extent of calcidiol 1-monooxygenase activity. Calcidiol 1-monooxygenase activity is the catalysis of the reaction: calcidiol + NADPH + H+ + O2 = calcitriol + NADP+ + H2O.
    GO:0010977    negative regulation of neuron projection development    Any process that decreases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    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: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:0070105    positive regulation of interleukin-6-mediated signaling pathway    Any process that increases the rate, frequency or extent of the series of molecular events generated as a consequence of interleukin-6 binding to a cell surface receptor.
    GO:0051569    regulation of histone H3-K4 methylation    Any process that modulates the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 4 of histone H3.
    GO:0050767    regulation of neurogenesis    Any process that modulates the frequency, rate or extent of neurogenesis, the origin and formation of neurons.
    GO:0034121    regulation of toll-like receptor signaling pathway    Any process that modulates the frequency, rate, or extent of toll-like receptor signaling pathway.
    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:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    GO:0016604    nuclear body    Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins.
    GO:0016363    nuclear matrix    The dense fibrillar network lying on the inner side of the nuclear membrane.
    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:0017053    transcriptional repressor complex    A protein complex that possesses activity that prevents or downregulates transcription.

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