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(-) Description

Title :  PU.1 ETS DOMAIN-DNA COMPLEX
 
Authors :  R. Kodandapani, F. Pio, C. Z. Ni, G. Piccialli, M. Klemsz, S. Mckercher, K. R. Ely
Date :  08 Jul 96  (Deposition) - 12 Feb 97  (Release) - 15 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,E  (1x)
Biol. Unit 2:  C,D,F  (1x)
Keywords :  Complex (Transcription Regulating-Dna), Oncogene, Transforming Protein, Dna- Binding, Activator, Nuclear Protein, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Kodandapani, F. Pio, C. Z. Ni, G. Piccialli, M. Klemsz, S. Mckercher R. A. Maki, K. R. Ely
A New Pattern For Helix-Turn-Helix Recognition Revealed By The Pu. 1 Ets-Domain-Dna Complex.
Nature V. 380 456 1996
PubMed-ID: 8602247  |  Reference-DOI: 10.1038/380456A0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'-D(*AP*AP*AP*AP*AP*GP*GP*GP*GP*AP*AP*GP*TP*GP*GP*G)- 3')
    Chains: A, C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 2 - DNA (5'-D(*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*CP*CP*TP*TP*TP*T)- 3')
    Chains: B, D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - PROTEIN (TRANSCRIPTION FACTOR PU.1 (TF PU.1))
    Chains: E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB  E 
Biological Unit 2 (1x):   CD F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1PUE)

(-) Sites  (0, 0)

(no "Site" information available for 1PUE)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 6)

Asymmetric Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ETS_DOMAIN_3PS50061 Ets-domain profile.SPI1_MOUSE172-255
 		  2E:172-255
F:172-255
2ETS_DOMAIN_1PS00345 Ets-domain signature 1.SPI1_MOUSE174-182
 		  2E:174-182
F:174-182
3ETS_DOMAIN_2PS00346 Ets-domain signature 2.SPI1_MOUSE222-237
 		  2E:222-237
F:222-237
Biological Unit 1 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ETS_DOMAIN_3PS50061 Ets-domain profile.SPI1_MOUSE172-255
 		  1E:172-255
-
2ETS_DOMAIN_1PS00345 Ets-domain signature 1.SPI1_MOUSE174-182
 		  1E:174-182
-
3ETS_DOMAIN_2PS00346 Ets-domain signature 2.SPI1_MOUSE222-237
 		  1E:222-237
-
Biological Unit 2 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ETS_DOMAIN_3PS50061 Ets-domain profile.SPI1_MOUSE172-255
 		  1-
F:172-255
2ETS_DOMAIN_1PS00345 Ets-domain signature 1.SPI1_MOUSE174-182
 		  1-
F:174-182
3ETS_DOMAIN_2PS00346 Ets-domain signature 2.SPI1_MOUSE222-237
 		  1-
F:222-237

(-) Exons   (0, 0)

(no "Exon" information available for 1PUE)

(-) Sequences/Alignments

Asymmetric 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:DNA  Length:16
                                                
                 1pue A   1 AAAAAGGGGAAGTGGG  16
                                    10      


Chain B from PDB  Type:DNA  Length:16
                                                
                 1pue B  17 TCCCACTTCCCCTTTT  32
                                    26      


Chain C from PDB  Type:DNA  Length:16
                                                
                 1pue C   1 AAAAAGGGGAAGTGGG  16
                                    10      


Chain D from PDB  Type:DNA  Length:16
                                                
                 1pue D  17 TCCCACTTCCCCTTTT  32
                                    26      


Chain E from PDB  Type:PROTEIN  Length:88
 aligned with SPI1_MOUSE | P17433 from UniProtKB/Swiss-Prot  Length:272

    Alignment length:88
                                   180       190       200       210       220       230       240       250        
           SPI1_MOUSE   171 KIRLYQFLLDLLRSGDMKDSIWWVDKDKGTFQFSSKHKEALAHRWGIQKGNRKKMTYQKMARALRNYGKTGEVKKVKKKLTYQFSGEV 258
               SCOP domains d1puee_ E: Transcription factor PU.1, residues 171-259                                   SCOP domains
               CATH domains 1pueE00 E:171-258 'winged helix' repressor DNA binding domain                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh......eeeee....eeee....hhhhhhhhhhhh.......hhhhhhhhhhhhhh..eee.....eeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -ETS_DOMAIN_3  PDB: E:172-255 UniProt: 172-255                                       --- PROSITE (1)
                PROSITE (2) ---ETS_DOMAI---------------------------------------ETS_DOMAIN_2    --------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 1pue E 171 KIRLYQFLLDLLRSGDMKDSIWWVDKDKGTFQFSSKHKEALAHRWGIQKGNRKKMTYEKMARALRNYGKTGEVKKVKKKLTYQFSGEV 258
                                   180       190       200       210       220       230       240       250        


Chain F from PDB  Type:PROTEIN  Length:89
 aligned with SPI1_MOUSE | P17433 from UniProtKB/Swiss-Prot  Length:272

    Alignment length:89
                                   180       190       200       210       220       230       240       250         
           SPI1_MOUSE   171 KIRLYQFLLDLLRSGDMKDSIWWVDKDKGTFQFSSKHKEALAHRWGIQKGNRKKMTYQKMARALRNYGKTGEVKKVKKKLTYQFSGEVL 259
               SCOP domains d1puef_ F: Transcription factor PU.1, residues 171-259                                    SCOP domains
               CATH domains 1pueF00 F:171-259 'winged helix' repressor DNA binding domain                             CATH domains
           Pfam domains (1) Ets-1pueF01 F:171-257                                                                  -- Pfam domains (1)
           Pfam domains (2) Ets-1pueF02 F:171-257                                                                  -- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhh.......eeeee....eeee....hhhhhhhhhhhh.......hhhhhhhhhhhhhh..eee.....eeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -ETS_DOMAIN_3  PDB: F:172-255 UniProt: 172-255                                       ---- PROSITE (1)
                PROSITE (2) ---ETS_DOMAI---------------------------------------ETS_DOMAIN_2    ---------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 1pue F 171 KIRLYQFLLDLLRSGDMKDSIWWVDKDKGTFQFSSKHKEALAHRWGIQKGNRKKMTYEKMARALRNYGKTGEVKKVKKKLTYQFSGEVL 259
                                   180       190       200       210       220       230       240       250
   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, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: HTH (544)
(-)
Family: Ets (14)
(-)
Mus musculus (Mouse) (8)
1aEts-1pueF01F:171-257
1bEts-1pueF02F:171-257

(-) Gene Ontology  (46, 46)

Asymmetric Unit(hide GO term definitions)
Chain E,F   (SPI1_MOUSE | P17433)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0051525    NFAT protein binding    Interacting selectively and non-covalently with NFAT (nuclear factor of activated T cells) proteins, a family of transcription factors. NFAT proteins have crucial roles in the development and function of the immune system.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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:0000979    RNA polymerase II core promoter sequence-specific DNA binding    Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase II basal transcription machinery.
    GO:0000980    RNA polymerase II distal enhancer sequence-specific DNA binding    Interacting selectively and non-covalently with a RNA polymerase II (Pol II) distal enhancer. In mammalian cells, enhancers are distal sequences that increase the utilization of some promoters, and can function in either orientation and in any location (upstream or downstream) relative to the core promoter.
    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:0001047    core promoter binding    Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. 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: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:0000982    transcription factor 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 modulate transcription by RNAP II.
    GO:0003705    transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in a distal enhancer region for RNA polymerase II (RNAP II) in order to modulate transcription by RNAP II.
    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:0001077    transcriptional activator 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 activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
    GO:0001205    transcriptional activator activity, RNA polymerase II distal enhancer sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in a distal enhancer 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: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:0060033    anatomical structure regression    The developmental process in which an anatomical stucture is destroyed as a part of its normal progression.
    GO:1902262    apoptotic process involved in blood vessel morphogenesis    Any apoptotic process that is involved in blood vessel morphogenesis.
    GO:0071361    cellular response to ethanol    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 ethanol stimulus.
    GO:0030218    erythrocyte differentiation    The process in which a myeloid precursor cell acquires specializes features of an erythrocyte.
    GO:0030851    granulocyte differentiation    The process in which a myeloid precursor cell acquires the specialized features of a granulocyte. Granulocytes are a class of leukocytes characterized by the presence of granules in their cytoplasm. These cells are active in allergic immune reactions such as arthritic inflammation and rashes. This class includes basophils, eosinophils and neutrophils.
    GO:0043966    histone H3 acetylation    The modification of histone H3 by the addition of an acetyl group.
    GO:0044027    hypermethylation of CpG island    An increase in the epigenetic methylation of cytosine and adenosine residues in a CpG island in DNA. CpG islands are genomic regions that contain a high frequency of the CG dinucleotide and are often associated with the transcription start site of genes.
    GO:0030098    lymphocyte differentiation    The process in which a relatively unspecialized precursor cell acquires specialized features of a lymphocyte. A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin.
    GO:0002320    lymphoid progenitor cell differentiation    The process in which a precursor cell type acquires the specialized features of a lymphoid progenitor cell. Lymphoid progenitor cells include progenitor cells for any of the lymphoid lineages.
    GO:0030225    macrophage differentiation    The process in which a relatively unspecialized monocyte acquires the specialized features of a macrophage.
    GO:0043011    myeloid dendritic cell differentiation    The process in which a monocyte acquires the specialized features of a dendritic cell, an immunocompetent cell of the lymphoid and hemopoietic systems and skin.
    GO:0002573    myeloid leukocyte differentiation    The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte lineage.
    GO:0045347    negative regulation of MHC class II biosynthetic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of MHC class II.
    GO:0045814    negative regulation of gene expression, epigenetic    Any epigenetic process that stops, prevents or reduces the rate of gene expression.
    GO:0090241    negative regulation of histone H4 acetylation    Any process that decreases the rate, frequency, or extent of histone H4 acetylation, the modification of histone H4 by the addition of an acetyl group.
    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:1902895    positive regulation of pri-miRNA transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of pri-miRNA transcription from RNA polymerase II promoter.
    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:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0045646    regulation of erythrocyte differentiation    Any process that modulates the frequency, rate or extent of erythrocyte differentiation.
    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:0035019    somatic stem cell population maintenance    Any process by which an organism retains a population of somatic stem cells, undifferentiated cells in the embryo or adult which can undergo unlimited division and give rise to cell types of the body other than those of the germ-line.
    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:0001944    vasculature development    The process whose specific outcome is the progression of the vasculature over time, from its formation to the mature structure. The vasculature is an interconnected tubular multi-tissue structure that contains fluid that is actively transported around the organism.
cellular component
    GO:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    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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