Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF IRF-3 BOUND TO THE PRDIII-I REGULATORY ELEMENT OF THE HUMAN INTERFERON-B ENHANCER
 
Authors :  C. R. Escalante, E. Nistal-Villan, S. Leyi, A. Garcia-Sastre, A. K. Aggarwal
Date :  12 Apr 07  (Deposition) - 30 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Interferon, Protein-Dna Complex, Transcription, Transcription Activator/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. R. Escalante, E. Nistal-Villan, L. Shen, A. Garcia-Sastre, A. K. Aggarwal
Structure Of Irf-3 Bound To The Prdiii-I Regulatory Element Of The Human Interferon-Beta Enhancer.
Mol. Cell V. 26 703 2007
PubMed-ID: 17560375  |  Reference-DOI: 10.1016/J.MOLCEL.2007.04.022
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INTERFERON REGULATORY FACTOR 3
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-15B
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: IRF-3 DNA BINDING DOMAIN
    Gene: IRF3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: IRF-3
 
Molecule 2 - PRDIII-I REGION OF HUMAN INTERFERON-B PROMOTER STRAND 1
    Chains: E
    Engineered: YES
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS
    Synthetic: YES
 
Molecule 3 - PRDIII-I REGION OF HUMAN INTERFERON-B PROMOTER STRAND 2
    Chains: F
    Engineered: YES
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2PI0)

(-) Sites  (0, 0)

(no "Site" information available for 2PI0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PI0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PI0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 8)

Asymmetric/Biological Unit (2, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_011901R96QIRF3_HUMANPolymorphism968457A/B/C/DR96Q
2UniProtVAR_049643Y107FIRF3_HUMANPolymorphism34745118A/B/C/DY107F
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 8)

Asymmetric/Biological Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IRF_2PS51507 IRF tryptophan pentad repeat DNA-binding domain profile.IRF3_HUMAN5-111
 
 
 		  4A:5-110
B:5-111
C:5-110
D:5-111
2IRF_1PS00601 IRF tryptophan pentad repeat DNA-binding domain signature.IRF3_HUMAN26-58
 
 
 		  4A:26-58
B:26-58
C:26-58
D:26-58

(-) Exons   (2, 8)

Asymmetric/Biological Unit (2, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003771391aENSE00001741588chr19:50169132-50168888245IRF3_HUMAN-00--
1.2ENST000003771392ENSE00001192374chr19:50168103-50167931173IRF3_HUMAN1-55554A:5-55 (gaps)
B:1-55
C:4-55
D:3-55 (gaps)		51
55
52
53
1.3ENST000003771393ENSE00000720991chr19:50166771-50166600172IRF3_HUMAN56-113584A:56-110
B:56-112
C:56-110
D:56-111		55
57
55
56
1.4ENST000003771394ENSE00001762773chr19:50166515-5016644571IRF3_HUMAN113-136240--
1.5ENST000003771395ENSE00001662781chr19:50165874-50165682193IRF3_HUMAN137-201650--
1.6ENST000003771396ENSE00001759095chr19:50165585-50165205381IRF3_HUMAN201-3281280--
1.7bENST000003771397bENSE00001699705chr19:50164085-50163970116IRF3_HUMAN328-366390--
1.8bENST000003771398bENSE00001707173chr19:50163090-50162829262IRF3_HUMAN367-427610--

(-) 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:98
 aligned with IRF3_HUMAN | Q14653 from UniProtKB/Swiss-Prot  Length:427

    Alignment length:106
                                    14        24        34        44        54        64        74        84        94       104      
           IRF3_HUMAN     5 KPRILPWLVSQLDLGQLEGVAWVNKSRTRFRIPWKHGLRQDAQQEDFGIFQAWAEATGAYVPGRDKPDLPTWKRNFRSALNRKEGLRLAEDRSKDPHDPHKIYEFV 110
               SCOP domains d2pi0a_ A: Interferon regulatory factor         3, IRF-3                                                   SCOP domains
               CATH domains --2pi0A01 A:7-110 'winged helix' repres        sor DNA binding domain                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.....ee......eeeee......--------hhhhhhhhhh..........hhhhhhhhhhhhhhhh...eeeeee.......eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------Q----------F--- SAPs(SNPs)
                PROSITE (1) IRF_2  PDB: A:5-110 UniProt: 5-111                                                                         PROSITE (1)
                PROSITE (2) ---------------------IRF_1  PDB: A:26-58              ---------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.2  PDB: A:5-55 (gaps) UniProt: 1-55         Exon 1.3  PDB: A:56-110 UniProt: 56-113 [INCOMPLETE]    Transcript 1
                 2pi0 A   5 KPRILPWLVSQLDLGQLEGVAWVNKSRTRFRIPWKHGLR--------GIFQAWAEATGAYVPGRDKPDLPTWKRNFRSALNRKEGLRLAEDRSKDPHDPHKIYEFV 110
                                    14        24        34        |-       |54        64        74        84        94       104      
                                                                 43       52                                                          


Chain B from PDB  Type:PROTEIN  Length:112
 aligned with IRF3_HUMAN | Q14653 from UniProtKB/Swiss-Prot  Length:427

    Alignment length:112
                                    10        20        30        40        50        60        70        80        90       100       110  
           IRF3_HUMAN     1 MGTPKPRILPWLVSQLDLGQLEGVAWVNKSRTRFRIPWKHGLRQDAQQEDFGIFQAWAEATGAYVPGRDKPDLPTWKRNFRSALNRKEGLRLAEDRSKDPHDPHKIYEFVNS 112
               SCOP domains d2pi0b_ B: Interferon regulatory factor 3, IRF-3                                                                 SCOP domains
               CATH domains ------2pi0B01 B:7-112 'winged helix' repressor DNA binding domain                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhh.....ee......eeeee..........hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------Q----------F----- SAPs(SNPs)
                PROSITE (1) ----IRF_2  PDB: B:5-111 UniProt: 5-111                                                                         - PROSITE (1)
                PROSITE (2) -------------------------IRF_1  PDB: B:26-58              ------------------------------------------------------ PROSITE (2)
               Transcript 1 Exon 1.2  PDB: B:1-55 UniProt: 1-55                    Exon 1.3  PDB: B:56-112 UniProt: 56-113 [INCOMPLETE]      Transcript 1
                 2pi0 B   1 MGTPKPRILPWLVSQLDLGQLEGVAWVNKSRTRFRIPWKHGLRQDAQQEDFGIFQAWAEATGAYVPGRDKPDLPTWKRNFRSALNRKEGLRLAEDRSKDPHDPHKIYEFVNS 112
                                    10        20        30        40        50        60        70        80        90       100       110  


Chain C from PDB  Type:PROTEIN  Length:107
 aligned with IRF3_HUMAN | Q14653 from UniProtKB/Swiss-Prot  Length:427

    Alignment length:107
                                    13        23        33        43        53        63        73        83        93       103       
           IRF3_HUMAN     4 PKPRILPWLVSQLDLGQLEGVAWVNKSRTRFRIPWKHGLRQDAQQEDFGIFQAWAEATGAYVPGRDKPDLPTWKRNFRSALNRKEGLRLAEDRSKDPHDPHKIYEFV 110
               SCOP domains d2pi0c_ C: Interferon regulatory factor 3, IRF-3                                                            SCOP domains
               CATH domains ---2pi0C01 C:7-110 'winged helix' repressor DNA binding domain                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh.....ee......eeeee..........hhhhhhhhhhhhhh..........hhhhhhhhhhhhhh....eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------Q----------F--- SAPs(SNPs)
                PROSITE (1) -IRF_2  PDB: C:5-110 UniProt: 5-111                                                                         PROSITE (1)
                PROSITE (2) ----------------------IRF_1  PDB: C:26-58              ---------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.2  PDB: C:4-55 UniProt: 1-55 [INCOMPLETE]    Exon 1.3  PDB: C:56-110 UniProt: 56-113 [INCOMPLETE]    Transcript 1
                 2pi0 C   4 PKPRILPWLVSQLDLGQLEGVAWVNKSRTRFRIPWKHGLRQDAQQEDFGIFQAWAEATGAYVPGRDKPDLPTWKRNFRSALNRKEGLRLAEDRSKDPHDPHKIYEFV 110
                                    13        23        33        43        53        63        73        83        93       103       


Chain D from PDB  Type:PROTEIN  Length:104
 aligned with IRF3_HUMAN | Q14653 from UniProtKB/Swiss-Prot  Length:427

    Alignment length:109
                                    12        22        32        42        52        62        72        82        92       102         
           IRF3_HUMAN     3 TPKPRILPWLVSQLDLGQLEGVAWVNKSRTRFRIPWKHGLRQDAQQEDFGIFQAWAEATGAYVPGRDKPDLPTWKRNFRSALNRKEGLRLAEDRSKDPHDPHKIYEFVN 111
               SCOP domains d2pi0d_ D: Interferon regulatory factor 3, I     RF-3                                                         SCOP domains
               CATH domains ----2pi0D01 D:7-111 'winged helix' repressor      DNA binding domain                                          CATH domains
           Pfam domains (1) --IRF-2pi0D01 D:5-111                                                                                         Pfam domains (1)
           Pfam domains (2) --IRF-2pi0D02 D:5-111                                                                                         Pfam domains (2)
           Pfam domains (3) --IRF-2pi0D03 D:5-111                                                                                         Pfam domains (3)
           Pfam domains (4) --IRF-2pi0D04 D:5-111                                                                                         Pfam domains (4)
         Sec.struct. author ....hhhhhhhhhhhhh.....ee......eeeee.........-----hhhhhhhhhh..........hhhhhhhhhhhhhhh...eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------Q----------F---- SAPs(SNPs)
                PROSITE (1) --IRF_2  PDB: D:5-111 UniProt: 5-111                                                                          PROSITE (1)
                PROSITE (2) -----------------------IRF_1  PDB: D:26-58              ----------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.2  PDB: D:3-55 (gaps) UniProt: 1-55           Exon 1.3  PDB: D:56-111 UniProt: 56-113 [INCOMPLETE]     Transcript 1
                 2pi0 D   3 TPKPRILPWLVSQLDLGQLEGVAWVNKSRTRFRIPWKHGLRQDA-----GIFQAWAEATGAYVPGRDKPDLPTWKRNFRSALNRKEGLRLAEDRSKDPHDPHKIYEFVN 111
                                    12        22        32        42   |    52        62        72        82        92       102         
                                                                      46    52                                                           


Chain E from PDB  Type:DNA  Length:32
                                                                
                 2pi0 E   2 CATAGGAAAACTGAAAGGGAGAAGTGAAAGTG  33
                                    11        21        31  


Chain F from PDB  Type:DNA  Length:32
                                                                
                 2pi0 F   2 CACTTTCACTTCTCCCTTTCAGTTTTCCTATG  33
                                    11        21        31
   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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: IRF] (4)
(-)
Family: IRF (4)
(-)
Homo sapiens (Human) (3)
1aIRF-2pi0D01D:5-111
1bIRF-2pi0D02D:5-111
1cIRF-2pi0D03D:5-111
1dIRF-2pi0D04D:5-111

(-) Gene Ontology  (43, 43)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (IRF3_HUMAN | Q14653)
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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    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:0003712    transcription cofactor activity    Interacting selectively and non-covalently with a regulatory transcription factor and also with the basal transcription machinery in order to modulate transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between regulatory transcription factors and the basal transcription machinery.
    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: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:0039530    MDA-5 signaling pathway    Any series of molecular signals generated as a consequence of the cytoplasmic pattern recognition receptor (PRR) MDA-5 (also known as IFIH1) binding to viral RNA. MDA-5 detects RNA synthesized during active viral replication and triggers a signaling pathway to protect the host against viral infection, for example by inducing the expression of antiviral cytokines.
    GO:0035666    TRIF-dependent toll-like receptor signaling pathway    Any series of molecular signals generated as a consequence of binding to a toll-like receptor where the TRIF adaptor mediates transduction of the signal. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response.
    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:0006974    cellular response to DNA damage 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 stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0071359    cellular response to dsRNA    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 double-stranded RNA stimulus.
    GO:0071222    cellular response to lipopolysaccharide    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 lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    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:0031663    lipopolysaccharide-mediated signaling pathway    A series of molecular signals initiated by the binding of a lipopolysaccharide (LPS) to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription. Lipopolysaccharides are major components of the outer membrane of Gram-negative bacteria, making them prime targets for recognition by the immune system.
    GO:0071888    macrophage apoptotic process    Any apoptotic process in a macrophage, a mononuclear phagocyte present in a variety of tissues.
    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:0032480    negative regulation of type I interferon production    Any process that stops, prevents, or reduces 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:0043123    positive regulation of I-kappaB kinase/NF-kappaB signaling    Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
    GO:0050715    positive regulation of cytokine secretion    Any process that activates or increases the frequency, rate or extent of the regulated release of cytokines from a cell.
    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: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:0097300    programmed necrotic cell death    A necrotic cell death process that results from the activation of endogenous cellular processes, such as signaling involving death domain receptors or Toll-like receptors.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0009617    response to bacterium    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a bacterium.
    GO:0043330    response to exogenous dsRNA    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an exogenous double-stranded RNA stimulus.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    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: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.
    GO:0060337    type I interferon signaling pathway    A series of molecular signals initiated by the binding of a type I interferon to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2pi0)
 
  Sites
(no "Sites" information available for 2pi0)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2pi0)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2pi0
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  IRF3_HUMAN | Q14653
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  IRF3_HUMAN | Q14653
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        IRF3_HUMAN | Q14653: 1j2f 1qwt 1t2k 1zoq 2o61 2o6g 3a77 3qu6 5jej 5jek 5jel 5jem 5jeo 5jer

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2PI0)