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(-) Description

Title :  INTERFERON REGULATORY FACTOR 1 (IRF-1) COMPLEX WITH DNA
 
Authors :  C. R. Escalante, J. Yie, D. Thanos, A. Aggarwal
Date :  12 Sep 97  (Deposition) - 25 Feb 98  (Release) - 15 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Complex (Dna-Binding Protein-Dna), Transcription Factor, Interferon Regulation, Helix-Turn-Helix, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. R. Escalante, J. Yie, D. Thanos, A. K. Aggarwal
Structure Of Irf-1 With Bound Dna Reveals Determinants Of Interferon Regulation.
Nature V. 391 103 1998
PubMed-ID: 9422515  |  Reference-DOI: 10.1038/34224
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (26-MER)
    Chains: C, D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 2 - PROTEIN (INTERFERON REGULATORY FACTOR 1)
    Cell Line: MOUSE FIBROBLAST L929
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-3A
    Expression System Strain: BL21 (DE3) PLYSS
    Expression System Taxid: 562
    Fragment: DNA-BINDING PROTEIN
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1IF1)

(-) Sites  (0, 0)

(no "Site" information available for 1IF1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1IF1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1IF1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1IF1)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IRF_1PS00601 IRF tryptophan pentad repeat DNA-binding domain signature.IRF1_MOUSE26-59
 		  2A:26-59
B:26-59

(-) Exons   (0, 0)

(no "Exon" information available for 1IF1)

(-) 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:105
 aligned with IRF1_MOUSE | P15314 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:105
                                    16        26        36        46        56        66        76        86        96       106     
           IRF1_MOUSE     7 RMRPWLEMQINSNQIPGLIWINKEEMIFQIPWKHAAKHGWDINKDACLFRSWAIHTGRYKAGEKEPDPKTWKANFRCAMNSLPDIEEVKDQSRNKGSSAVRVYRM 111
               SCOP domains d1if1a_ A: Interferon regulatory factor 1 (IRF-1)                                                         SCOP domains
               CATH domains 1if1A00 A:7-111 'winged helix' repressor DNA binding domain                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhh...........eeee.................hhhhhhhh............hhhhhhhhhhhhhh...eee...........eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------IRF_1  PDB: A:26-59 UniProt: 26-59---------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 1if1 A   7 RMRPWLEMQINSNQIPGLIWINKEEMIFQIPWKHAAKHGWDINKDACLFRSWAIHTGRYKAGEKEPDPKTWKANFRCAMNSLPDIEEVKDQSRNKGSSAVRVYRM 111
                                    16        26        36        46        56        66        76        86        96       106     


Chain B from PDB  Type:PROTEIN  Length:104
 aligned with IRF1_MOUSE | P15314 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:104
                                    17        27        37        47        57        67        77        87        97       107    
           IRF1_MOUSE     8 MRPWLEMQINSNQIPGLIWINKEEMIFQIPWKHAAKHGWDINKDACLFRSWAIHTGRYKAGEKEPDPKTWKANFRCAMNSLPDIEEVKDQSRNKGSSAVRVYRM 111
               SCOP domains d1if1b_ B: Interferon regulatory factor 1 (IRF-1)                                                        SCOP domains
               CATH domains 1if1B00 B:8-111 'winged helix' repressor DNA binding domain                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhh...........eeee.................hhhhhhhh............hhhhhhhhhhhhhh...eee...........eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------IRF_1  PDB: B:26-59 UniProt: 26-59---------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 1if1 B   8 MRPWLEMQINSNQIPGLIWINKEEMIFQIPWKHAAKHGWDINKDACLFRSWAIHTGRYKAGEKEPDPKTWKANFRCAMNSLPDIEEVKDQSRNKGSSAVRVYRM 111
                                    17        27        37        47        57        67        77        87        97       107    


Chain C from PDB  Type:DNA  Length:26
                                                          
                 1if1 C 200 GAGAAGTGAAAGTACTTTCACTTCTC 225
                                   209       219      


Chain D from PDB  Type:DNA  Length:26
                                                          
                 1if1 D 500 GAGAAGTGAAAGTACTTTCACTTCTC 525
                                   509       519
   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/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IF1)

(-) Gene Ontology  (39, 39)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (IRF1_MOUSE | P15314)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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: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:0000975    regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that regulates a DNA-based process. Such processes include transcription, DNA replication, and DNA repair.
    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: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.
biological process
    GO:0043374    CD8-positive, alpha-beta T cell differentiation    The process in which a relatively unspecialized T cell acquires specialized features of a mature CD8-positive, alpha-beta T cell.
    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:0007050    cell cycle arrest    A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).
    GO:0035458    cellular response to interferon-beta    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 interferon-beta stimulus. Interferon-beta is a type I interferon.
    GO:0071260    cellular response to mechanical stimulus    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 mechanical stimulus.
    GO:0051607    defense response to virus    Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0060333    interferon-gamma-mediated signaling pathway    A series of molecular signals initiated by the binding of interferon-gamma to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Interferon gamma is the only member of the type II interferon found so far.
    GO:0045629    negative regulation of T-helper 2 cell differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of T-helper 2 cell differentiation.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0045590    negative regulation of regulatory T cell differentiation    Any process that stops, prevents, or reduces the rate of differentiation of regulatory T cells.
    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:0045627    positive regulation of T-helper 1 cell differentiation    Any process that activates or increases the frequency, rate or extent of T-helper 1 cell differentiation.
    GO:0032728    positive regulation of interferon-beta production    Any process that activates or increases the frequency, rate, or extent of interferon-beta production.
    GO:0045084    positive regulation of interleukin-12 biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interleukin-12.
    GO:0032825    positive regulation of natural killer cell differentiation    Any process that activates or increases the frequency, rate or extent of natural killer cell differentiation.
    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:0032481    positive regulation of type I interferon production    Any process that activates or increases the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    GO:2000564    regulation of CD8-positive, alpha-beta T cell proliferation    Any process that modulates the frequency, rate or extent of CD8-positive, alpha-beta T cell proliferation.
    GO:0034124    regulation of MyD88-dependent toll-like receptor signaling pathway    Any process that modulates the frequency, rate, or extent of MyD88-dependent toll-like receptor signaling pathway.
    GO:0002819    regulation of adaptive immune response    Any process that modulates the frequency, rate, or extent of an adaptive immune response.
    GO:0010468    regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0050776    regulation of immune response    Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
    GO:0045088    regulation of innate immune response    Any process that modulates the frequency, rate or extent of the innate immune response, the organism's first line of defense against infection.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.

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