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(-) Description

Title :  CRYSTAL STRUCTURE OF AN IRF-2/DNA COMPLEX.
 
Authors :  Y. Fujii, T. Shimizu, M. Kusumoto, Y. Kyogoku, T. Taniguchi, T. Hakoshima
Date :  30 May 99  (Deposition) - 08 Oct 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,F,G,H  (1x)
Biol. Unit 2:  B,E,I,J  (1x)
Biol. Unit 3:  C,D,K,L  (1x)
Keywords :  Transcription Factor, Ifn Induction, Irf Family, Gene Regulation/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Fujii, T. Shimizu, M. Kusumoto, Y. Kyogoku, T. Taniguchi, T. Hakoshima
Crystal Structure Of An Irf-Dna Complex Reveals Novel Dna Recognition And Cooperative Binding To A Tandem Repeat Of Core Sequences.
Embo J. V. 18 5028 1999
PubMed-ID: 10487755  |  Reference-DOI: 10.1093/EMBOJ/18.18.5028
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'-D(P*AP*AP*GP*TP*GP*AP*AP*AP*GP*(5IU) P*GP*A)-3')
    ChainsA, B, C
    EngineeredYES
    SyntheticYES
 
Molecule 2 - DNA (5'- D(*TP*TP*CP*AP*CP*TP*TP*TP*CP*AP*CP*(5IU)P*T)-3')
    ChainsD, E, F
    EngineeredYES
    SyntheticYES
 
Molecule 3 - INTERFERON REGULATORY FACTOR 2
    ChainsG, H, I, J, K, L
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidT7
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentDNA-BINDING DOMAIN
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymIRF-2

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit ABCDEFGHIJKL
Biological Unit 1 (1x)A    FGH    
Biological Unit 2 (1x) B  E   IJ  
Biological Unit 3 (1x)  CD      KL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
15IU6Mod. Nucleotide5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2K6Ligand/IonPOTASSIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
15IU2Mod. Nucleotide5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2K-1Ligand/IonPOTASSIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
15IU2Mod. Nucleotide5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2K-1Ligand/IonPOTASSIUM ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
15IU2Mod. Nucleotide5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2K-1Ligand/IonPOTASSIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET G:85 , ASN G:86 , LEU G:88 , ILE G:91BINDING SITE FOR RESIDUE K G 4001
2AC2SOFTWAREMET L:2085 , ASN L:2086 , LEU L:2088 , ILE L:2091BINDING SITE FOR RESIDUE K L 4002
3AC3SOFTWAREMET I:485 , ASN I:486 , LEU I:488 , ILE I:491BINDING SITE FOR RESIDUE K I 4003
4AC4SOFTWAREMET K:885 , ASN K:886 , LEU K:888 , ILE K:891BINDING SITE FOR RESIDUE K K 4004
5AC5SOFTWAREMET J:685 , ASN J:686 , LEU J:688 , ILE J:691BINDING SITE FOR RESIDUE K J 4005
6AC6SOFTWAREMET H:285 , ASN H:286 , LEU H:288 , ILE H:291BINDING SITE FOR RESIDUE K H 4006

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu I:512 -Pro I:513

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 12)

Asymmetric Unit (2, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IRF_2PS51507 IRF tryptophan pentad repeat DNA-binding domain profile.IRF2_MOUSE5-113
 
 
 
 
 
  6G:5-113
H:205-313
I:405-513
J:605-713
K:805-913
L:2005-2113
2IRF_1PS00601 IRF tryptophan pentad repeat DNA-binding domain signature.IRF2_MOUSE26-59
 
 
 
 
 
  6G:26-59
H:226-259
I:426-459
J:626-659
K:826-859
L:2026-2059
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IRF_2PS51507 IRF tryptophan pentad repeat DNA-binding domain profile.IRF2_MOUSE5-113
 
 
 
 
 
  2G:5-113
H:205-313
-
-
-
-
2IRF_1PS00601 IRF tryptophan pentad repeat DNA-binding domain signature.IRF2_MOUSE26-59
 
 
 
 
 
  2G:26-59
H:226-259
-
-
-
-
Biological Unit 2 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IRF_2PS51507 IRF tryptophan pentad repeat DNA-binding domain profile.IRF2_MOUSE5-113
 
 
 
 
 
  2-
-
I:405-513
J:605-713
-
-
2IRF_1PS00601 IRF tryptophan pentad repeat DNA-binding domain signature.IRF2_MOUSE26-59
 
 
 
 
 
  2-
-
I:426-459
J:626-659
-
-
Biological Unit 3 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IRF_2PS51507 IRF tryptophan pentad repeat DNA-binding domain profile.IRF2_MOUSE5-113
 
 
 
 
 
  2-
-
-
-
K:805-913
L:2005-2113
2IRF_1PS00601 IRF tryptophan pentad repeat DNA-binding domain signature.IRF2_MOUSE26-59
 
 
 
 
 
  2-
-
-
-
K:826-859
L:2026-2059

(-) Exons   (0, 0)

(no "Exon" information available for 2IRF)

(-) 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:12
                                             
                2irf A 1001 AAGTGAAAGuGA 1012
                                  1010  
                                  1010-5IU

Chain B from PDB  Type:DNA  Length:12
                                             
                2irf B 1013 AAGTGAAAGuGA 1024
                                  1022  
                                  1022-5IU

Chain C from PDB  Type:DNA  Length:12
                                             
                2irf C 1025 AAGTGAAAGuGA 1036
                                  1034  
                                  1034-5IU

Chain D from PDB  Type:DNA  Length:13
                                              
                2irf D 1100 TTCACTTTCACuT 1112
                                  1109 | 
                                    1111-5IU

Chain E from PDB  Type:DNA  Length:12
                                             
                2irf E 1113 TCACTTTCACuT 1124
                                  1122| 
                                   1123-5IU

Chain F from PDB  Type:DNA  Length:13
                                              
                2irf F 1124 TTCACTTTCACuT 1136
                                  1133 | 
                                    1135-5IU

Chain G from PDB  Type:PROTEIN  Length:109
 aligned with IRF2_MOUSE | P23906 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:109
                                    14        24        34        44        54        64        74        84        94       104         
          IRF2_MOUSE      5 RMRMRPWLEEQINSNTIPGLKWLNKEKKIFQIPWMHAARHGWDVEKDAPLFRNWAIHTGKHQPGIDKPDPKTWKANFRCAMNSLPDIEEVKDRSIKKGNNAFRVYRMLP  113
               SCOP domains d2irfg_ G: Interferon regulatory factor-2, IRF-2                                                              SCOP domains
               CATH domains 2irfG00 G:5-113 'winged helix' repressor DNA binding domain                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh......eeee....eeeee.........hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh..eeee...........eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) IRF_2  PDB: G:5-113 UniProt: 5-113                                                                            PROSITE (1)
                PROSITE (2) ---------------------IRF_1  PDB: G:26-59 UniProt: 26-59------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                2irf G    5 RMRMRPWLEEQINSNTIPGLKWLNKEKKIFQIPWMHAARHGWDVEKDAPLFRNWAIHTGKHQPGIDKPDPKTWKANFRCAMNSLPDIEEVKDRSIKKGNNAFRVYRMLP  113
                                    14        24        34        44        54        64        74        84        94       104         

Chain H from PDB  Type:PROTEIN  Length:109
 aligned with IRF2_MOUSE | P23906 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:109
                                    14        24        34        44        54        64        74        84        94       104         
          IRF2_MOUSE      5 RMRMRPWLEEQINSNTIPGLKWLNKEKKIFQIPWMHAARHGWDVEKDAPLFRNWAIHTGKHQPGIDKPDPKTWKANFRCAMNSLPDIEEVKDRSIKKGNNAFRVYRMLP  113
               SCOP domains d2irfh_ H: Interferon regulatory factor-2, IRF-2                                                              SCOP domains
               CATH domains 2irfH00 H:205-313 'winged helix' repressor DNA binding domain                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.....eeee....eeeee.........hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh..eeee...........eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) IRF_2  PDB: H:205-313 UniProt: 5-113                                                                          PROSITE (1)
                PROSITE (2) ---------------------IRF_1  PDB: H:226-259             ------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                2irf H  205 RMRMRPWLEEQINSNTIPGLKWLNKEKKIFQIPWMHAARHGWDVEKDAPLFRNWAIHTGKHQPGIDKPDPKTWKANFRCAMNSLPDIEEVKDRSIKKGNNAFRVYRMLP  313
                                   214       224       234       244       254       264       274       284       294       304         

Chain I from PDB  Type:PROTEIN  Length:109
 aligned with IRF2_MOUSE | P23906 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:109
                                    14        24        34        44        54        64        74        84        94       104         
          IRF2_MOUSE      5 RMRMRPWLEEQINSNTIPGLKWLNKEKKIFQIPWMHAARHGWDVEKDAPLFRNWAIHTGKHQPGIDKPDPKTWKANFRCAMNSLPDIEEVKDRSIKKGNNAFRVYRMLP  113
               SCOP domains d2irfi_ I: Interferon regulatory factor-2, IRF-2                                                              SCOP domains
               CATH domains 2irfI00 I:405-513 'winged helix' repressor DNA binding domain                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.....eeee....eeeee.........hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh..eeee...........eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) IRF_2  PDB: I:405-513 UniProt: 5-113                                                                          PROSITE (1)
                PROSITE (2) ---------------------IRF_1  PDB: I:426-459             ------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                2irf I  405 RMRMRPWLEEQINSNTIPGLKWLNKEKKIFQIPWMHAARHGWDVEKDAPLFRNWAIHTGKHQPGIDKPDPKTWKANFRCAMNSLPDIEEVKDRSIKKGNNAFRVYRMLP  513
                                   414       424       434       444       454       464       474       484       494       504         

Chain J from PDB  Type:PROTEIN  Length:109
 aligned with IRF2_MOUSE | P23906 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:109
                                    14        24        34        44        54        64        74        84        94       104         
          IRF2_MOUSE      5 RMRMRPWLEEQINSNTIPGLKWLNKEKKIFQIPWMHAARHGWDVEKDAPLFRNWAIHTGKHQPGIDKPDPKTWKANFRCAMNSLPDIEEVKDRSIKKGNNAFRVYRMLP  113
               SCOP domains d2irfj_ J: Interferon regulatory factor-2, IRF-2                                                              SCOP domains
               CATH domains 2irfJ00 J:605-713 'winged helix' repressor DNA binding domain                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh......eeee....eeeee.........hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh..eeee...........eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) IRF_2  PDB: J:605-713 UniProt: 5-113                                                                          PROSITE (1)
                PROSITE (2) ---------------------IRF_1  PDB: J:626-659             ------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                2irf J  605 RMRMRPWLEEQINSNTIPGLKWLNKEKKIFQIPWMHAARHGWDVEKDAPLFRNWAIHTGKHQPGIDKPDPKTWKANFRCAMNSLPDIEEVKDRSIKKGNNAFRVYRMLP  713
                                   614       624       634       644       654       664       674       684       694       704         

Chain K from PDB  Type:PROTEIN  Length:109
 aligned with IRF2_MOUSE | P23906 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:109
                                    14        24        34        44        54        64        74        84        94       104         
          IRF2_MOUSE      5 RMRMRPWLEEQINSNTIPGLKWLNKEKKIFQIPWMHAARHGWDVEKDAPLFRNWAIHTGKHQPGIDKPDPKTWKANFRCAMNSLPDIEEVKDRSIKKGNNAFRVYRMLP  113
               SCOP domains d2irfk_ K: Interferon regulatory factor-2, IRF-2                                                              SCOP domains
               CATH domains 2irfK00 K:805-913 'winged helix' repressor DNA binding domain                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh......eeee....eeeee.........hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh..eeee...........eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) IRF_2  PDB: K:805-913 UniProt: 5-113                                                                          PROSITE (1)
                PROSITE (2) ---------------------IRF_1  PDB: K:826-859             ------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                2irf K  805 RMRMRPWLEEQINSNTIPGLKWLNKEKKIFQIPWMHAARHGWDVEKDAPLFRNWAIHTGKHQPGIDKPDPKTWKANFRCAMNSLPDIEEVKDRSIKKGNNAFRVYRMLP  913
                                   814       824       834       844       854       864       874       884       894       904         

Chain L from PDB  Type:PROTEIN  Length:109
 aligned with IRF2_MOUSE | P23906 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:109
                                    14        24        34        44        54        64        74        84        94       104         
          IRF2_MOUSE      5 RMRMRPWLEEQINSNTIPGLKWLNKEKKIFQIPWMHAARHGWDVEKDAPLFRNWAIHTGKHQPGIDKPDPKTWKANFRCAMNSLPDIEEVKDRSIKKGNNAFRVYRMLP  113
               SCOP domains d2irfl_ L: Interferon regulatory factor-2, IRF-2                                                              SCOP domains
               CATH domains 2irfL00 L:2005-2113 'winged helix' repressor DNA binding domain                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.....eeee....eeeee.........hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh..eeee...........eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) IRF_2  PDB: L:2005-2113 UniProt: 5-113                                                                        PROSITE (1)
                PROSITE (2) ---------------------IRF_1  PDB: L:2026-2059           ------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                2irf L 2005 RMRMRPWLEEQINSNTIPGLKWLNKEKKIFQIPWMHAARHGWDVEKDAPLFRNWAIHTGKHQPGIDKPDPKTWKANFRCAMNSLPDIEEVKDRSIKKGNNAFRVYRMLP 2113
                                  2014      2024      2034      2044      2054      2064      2074      2084      2094      2104         

   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, 6)

Asymmetric Unit

(-) CATH Domains  (1, 6)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain G,H,I,J,K,L   (IRF2_MOUSE | P23906)
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: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: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.
biological process
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    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: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:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    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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 Related Entries

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

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        IRF2_MOUSE | P239061irf 1irg

(-) Related Entries Specified in the PDB File

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