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(-) Description

Title :  CRYSTAL STRUCTURE OF IRF-7 DBD APO FORM
 
Authors :  P. E. De Ioannes, C. R. Escalante, A. K. Aggarwal
Date :  23 Feb 11  (Deposition) - 01 Jun 11  (Release) - 01 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Helix-Turn-Helix, Gene Regulation, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. De Ioannes, C. R. Escalante, A. K. Aggarwal
Structures Of Apo Irf-3 And Irf-7 Dna Binding Domains: Effect Of Loop L1 On Dna Binding.
Nucleic Acids Res. V. 39 7300 2011
PubMed-ID: 21596780  |  Reference-DOI: 10.1093/NAR/GKR325

(-) Compounds

Molecule 1 - INTERFERON REGULATORY FACTOR 7
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)PLYS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: DNA BINDING DOMAIN
    Gene: IRF7
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: IRF-7

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2NA3Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2NA-1Ligand/IonSODIUM ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2NA-1Ligand/IonSODIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:99 , HIS A:100 , THR A:102 , PHE A:105 , HOH A:199BINDING SITE FOR RESIDUE NA A 135
2AC2SOFTWARELEU B:99 , THR B:102 , PHE B:105 , HOH B:162BINDING SITE FOR RESIDUE NA B 135
3AC3SOFTWARELEU B:107 , ARG B:108 , HOH B:278 , VAL C:116BINDING SITE FOR RESIDUE EDO B 136
4AC4SOFTWAREGLY B:18 , SER B:21 , SER B:22 , EDO B:138BINDING SITE FOR RESIDUE EDO B 137
5AC5SOFTWARESER B:21 , TRP B:30 , EDO B:137 , HOH B:271BINDING SITE FOR RESIDUE EDO B 138
6AC6SOFTWARELEU C:99 , THR C:102 , PHE C:105 , HOH C:145BINDING SITE FOR RESIDUE NA C 135
7AC7SOFTWARELEU C:11 , ASP C:14 , TRP C:68 , GLY C:72 , VAL C:73 , ALA C:80 , GLU C:84 , HOH C:194 , HOH C:252BINDING SITE FOR RESIDUE EDO C 136

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QU3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3QU3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QU3)

(-) PROSITE Motifs  (2, 6)

Asymmetric Unit (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IRF_2PS51507 IRF tryptophan pentad repeat DNA-binding domain profile.IRF7_MOUSE9-126
 
 		  3A:9-126
B:9-125
C:9-125
2IRF_1PS00601 IRF tryptophan pentad repeat DNA-binding domain signature.IRF7_MOUSE30-62
 
 		  3A:30-62
B:30-62
C:30-62
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IRF_2PS51507 IRF tryptophan pentad repeat DNA-binding domain profile.IRF7_MOUSE9-126
 
 		  1A:9-126
-
-
2IRF_1PS00601 IRF tryptophan pentad repeat DNA-binding domain signature.IRF7_MOUSE30-62
 
 		  1A:30-62
-
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IRF_2PS51507 IRF tryptophan pentad repeat DNA-binding domain profile.IRF7_MOUSE9-126
 
 		  1-
B:9-125
-
2IRF_1PS00601 IRF tryptophan pentad repeat DNA-binding domain signature.IRF7_MOUSE30-62
 
 		  1-
B:30-62
-
Biological Unit 3 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IRF_2PS51507 IRF tryptophan pentad repeat DNA-binding domain profile.IRF7_MOUSE9-126
 
 		  1-
-
C:9-125
2IRF_1PS00601 IRF tryptophan pentad repeat DNA-binding domain signature.IRF7_MOUSE30-62
 
 		  1-
-
C:30-62

(-) Exons   (0, 0)

(no "Exon" information available for 3QU3)

(-) 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:PROTEIN  Length:122
 aligned with IRF7_MOUSE | P70434 from UniProtKB/Swiss-Prot  Length:457

    Alignment length:122
                                    18        28        38        48        58        68        78        88        98       108       118       128  
           IRF7_MOUSE     9 RVLFGDWLLGEVSSGQYEGLQWLNEARTVFRVPWKHFGRRDLDEEDAQIFKAWAVARGRWPPSGVNLPPPEAEAAERRERRGWKTNFRCALHSTGRFILRQDNSGDPVDPHKVYELSRELGS 130
               SCOP domains d3qu3a_ A: automated matches                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.....ee......eeeee.........hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.......eeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) IRF_2  PDB: A:9-126 UniProt: 9-126                                                                                    ---- PROSITE (1)
                PROSITE (2) ---------------------IRF_1  PDB: A:30-62              -------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qu3 A   9 RVLFGDWLLGEVSSGQYEGLQWLNEARTVFRVPWKHFGRRDLDEEDAQIFKAWAVARGRWPPSGVNLPPPEAEAAERRERRGWKTNFRCALHSTGRFILRQDNSGDPVDPHKVYELSRELGS 130
                                    18        28        38        48        58        68        78        88        98       108       118       128  


Chain B from PDB  Type:PROTEIN  Length:117
 aligned with IRF7_MOUSE | P70434 from UniProtKB/Swiss-Prot  Length:457

    Alignment length:117
                                    18        28        38        48        58        68        78        88        98       108       118       
           IRF7_MOUSE     9 RVLFGDWLLGEVSSGQYEGLQWLNEARTVFRVPWKHFGRRDLDEEDAQIFKAWAVARGRWPPSGVNLPPPEAEAAERRERRGWKTNFRCALHSTGRFILRQDNSGDPVDPHKVYELS 125
               SCOP domains d3qu3b_ B: automated matches                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.....ee......eeeee.........hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) IRF_2  PDB: B:9-125 UniProt: 9-126                                                                                    PROSITE (1)
                PROSITE (2) ---------------------IRF_1  PDB: B:30-62              --------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3qu3 B   9 RVLFGDWLLGEVSSGQYEGLQWLNEARTVFRVPWKHFGRRDLDEEDAQIFKAWAVARGRWPPSGVNLPPPEAEAAERRERRGWKTNFRCALHSTGRFILRQDNSGDPVDPHKVYELS 125
                                    18        28        38        48        58        68        78        88        98       108       118       


Chain C from PDB  Type:PROTEIN  Length:118
 aligned with IRF7_MOUSE | P70434 from UniProtKB/Swiss-Prot  Length:457

    Alignment length:118
                                    17        27        37        47        57        67        77        87        97       107       117        
           IRF7_MOUSE     8 QRVLFGDWLLGEVSSGQYEGLQWLNEARTVFRVPWKHFGRRDLDEEDAQIFKAWAVARGRWPPSGVNLPPPEAEAAERRERRGWKTNFRCALHSTGRFILRQDNSGDPVDPHKVYELS 125
               SCOP domains d3qu3c_ C: automated matches                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -IRF-3qu3C01 C:9-125                                                                                                   Pfam domains (1)
           Pfam domains (2) -IRF-3qu3C02 C:9-125                                                                                                   Pfam domains (2)
           Pfam domains (3) -IRF-3qu3C03 C:9-125                                                                                                   Pfam domains (3)
         Sec.struct. author ...hhhhhhhhhhhhh.....ee......eeeee..........hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -IRF_2  PDB: C:9-125 UniProt: 9-126                                                                                    PROSITE (1)
                PROSITE (2) ----------------------IRF_1  PDB: C:30-62              --------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3qu3 C   8 QRVLFGDWLLGEVSSGQYEGLQWLNEARTVFRVPWKHFGRRDLDEEDAQIFKAWAVARGRWPPSGVNLPPPEAEAAERRERRGWKTNFRCALHSTGRFILRQDNSGDPVDPHKVYELS 125
                                    17        27        37        47        57        67        77        87        97       107       117
   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 Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QU3)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: no clan defined [family: IRF] (4)
(-)
Family: IRF (4)
(-)
Mus musculus (Mouse) (1)
1aIRF-3qu3C01C:9-125
1bIRF-3qu3C02C:9-125
1cIRF-3qu3C03C:9-125

(-) Gene Ontology  (27, 27)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (IRF7_MOUSE | P70434)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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: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: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: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.
biological process
    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:0016064    immunoglobulin mediated immune response    An immune response mediated by immunoglobulins, whether cell-bound or in solution.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0032607    interferon-alpha production    The appearance of interferon-alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
    GO:0032608    interferon-beta production    The appearance of interferon-beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
    GO:0032727    positive regulation of interferon-alpha production    Any process that activates or increases the frequency, rate, or extent of interferon-alpha production.
    GO:0032728    positive regulation of interferon-beta production    Any process that activates or increases the frequency, rate, or extent of interferon-beta production.
    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:0060340    positive regulation of type I interferon-mediated signaling pathway    Any process that increases the rate, frequency or extent of a type I interferon-mediated signaling pathway. A type I interferon-mediated signaling pathway is the series of molecular events generated as a consequence of a type I interferon binding to a cell surface receptor.
    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:0034127    regulation of MyD88-independent toll-like receptor signaling pathway    Any process that modulates the frequency, rate, or extent of MyD88-independent 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: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:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0045351    type I interferon biosynthetic process    The chemical reactions and pathways resulting in the formation of any type I interferon. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
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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3qu6