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(-) Description

Title :  SOLUTION STRUCTURE OF THE C-TERMINAL DOMAIN OF CHICKEN GATA-1 BOUND TO DNA, NMR, REGULARIZED MEAN STRUCTURE
 
Authors :  G. M. Clore, N. Tjandra, M. Starich, J. G. Omichinski, A. M. Gronenborn
Date :  07 Nov 97  (Deposition) - 28 Jan 98  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C
Keywords :  Dna Binding Protein, Transcription Factor, Zinc Binding Domain, Complex (Transcription Regulation/Dna), Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Tjandra, J. G. Omichinski, A. M. Gronenborn, G. M. Clore, A. Bax
Use Of Dipolar 1H-15N And 1H-13C Couplings In The Structure Determination Of Magnetically Oriented Macromolecules In Solution.
Nat. Struct. Biol. V. 4 732 1997
PubMed-ID: 9303001  |  Reference-DOI: 10.1038/NSB0997-732
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*GP*TP*TP*GP*CP*AP*GP*AP*TP*AP*AP*AP*CP*AP*TP*T)-3')
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - DNA (5'- D(*AP*AP*TP*GP*TP*TP*TP*AP*TP*CP*TP*GP*CP*AP*AP*C)-3')
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - ERYTHROID TRANSCRIPTION FACTOR GATA-1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: C-TERMINAL DOMAIN
    Organism Common: CHICKEN
    Organism Scientific: GALLUS GALLUS
    Organism Taxid: 9031

 Structural Features

(-) Chains, Units

  
NMR Structure : 

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:7 , CYS A:10 , CYS A:28 , CYS A:31BINDING SITE FOR RESIDUE ZN A 67

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GATA_ZN_FINGER_2PS50114 GATA-type zinc finger domain profile.GATA1_CHICK104-159
158-211		  1-
A:1-54
2GATA_ZN_FINGER_1PS00344 GATA-type zinc finger domain.GATA1_CHICK110-134
164-188		  1-
A:7-31

(-) Exons   (0, 0)

(no "Exon" information available for 2GAT)

(-) 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:66
 aligned with GATA1_CHICK | P17678 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:66
                                   167       177       187       197       207       217      
          GATA1_CHICK   158 KRAGTVCSNCQTSTTTLWRRSPMGDPVCNACGLYYKLHQVNRPLTMRKDGIQTRNRKVSSKGKKRR 223
               SCOP domains d2gata_ A: Erythroid transcription factor GATA-1                   SCOP domains
               CATH domains 2gatA00 A:1-66 Erythroid Transcription Factor GATA-1, subunit A    CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .................eee.....eeehhhhhhhhhh.....hhh.................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) GA----GATA_ZN_FINGER_1         ----------------------------------- PROSITE (1)
                PROSITE (2) GATA_ZN_FINGER_2  PDB: A:1-54 UniProt: 158-211        ------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------ Transcript
                 2gat A   1 KRAGTVCSNCQTSTTTLWRRSPMGDPVCNACGLYYKLHQVNRPLTMRKDGIQTRNRKVSSKGKKRR  66
                                    10        20        30        40        50        60      


Chain B from PDB  Type:DNA  Length:16
                                                
                 2gat B 101 GTTGCAGATAAACATT 116
                                   110      


Chain C from PDB  Type:DNA  Length:16
                                                
                 2gat C 117 AATGTTTATCTGCAAC 132
                                   126
   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
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (28, 28)

NMR Structure(hide GO term definitions)
Chain A   (GATA1_CHICK | P17678)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0001085    RNA polymerase II transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription factor, any protein required to initiate or regulate transcription by RNA polymerase II.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    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: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: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.
    GO:0001228    transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in the transcription regulatory region for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0048646    anatomical structure formation involved in morphogenesis    The developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
    GO:0009887    animal organ morphogenesis    Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
    GO:0030221    basophil differentiation    The process in which a relatively unspecialized myeloid precursor cell acquires specialized features of a basophil cell.
    GO:0048468    cell development    The process whose specific outcome is the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate.
    GO:0045165    cell fate commitment    The commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field.
    GO:0048565    digestive tract development    The process whose specific outcome is the progression of the digestive tract over time, from its formation to the mature structure. The digestive tract is the anatomical structure through which food passes and is processed.
    GO:0030222    eosinophil differentiation    The process in which a relatively unspecialized myeloid precursor cell acquires the specializes features of an eosinophil.
    GO:0048821    erythrocyte development    The process whose specific outcome is the progression of an erythrocyte over time, from its formation to the mature structure.
    GO:0030218    erythrocyte differentiation    The process in which a myeloid precursor cell acquires specializes features of an erythrocyte.
    GO:0007507    heart development    The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0030219    megakaryocyte differentiation    The process in which a myeloid precursor cell acquires specializes features of a megakaryocyte.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases 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:0009888    tissue development    The process whose specific outcome is the progression of a tissue over time, from its formation to the mature structure.
    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.
cellular component
    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

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

UniProtKB/Swiss-Prot
        GATA1_CHICK | P17678: 1gat 1gau 3gat

(-) Related Entries Specified in the PDB File

3gat ENSEMBLE OF 34 STRUCTURES