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(-) Description

Title :  TONEBP/DNA COMPLEX
 
Authors :  J. C. Stroud, C. Lopez-Rodriguez, A. Rao, L. Chen
Date :  10 May 01  (Deposition) - 01 Feb 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.86
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Beta Barrel, Protein-Dna Complex, Double Helix, Dna Encirclement, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. C. Stroud, C. Lopez-Rodriguez, A. Rao, L. Chen
Structure Of A Tonebp-Dna Complex Reveals Dna Encircled By A Transcription Factor.
Nat. Struct. Biol. V. 9 90 2002
PubMed-ID: 11780147  |  Reference-DOI: 10.1038/NSB749
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'- D(*TP*TP*GP*CP*TP*GP*GP*AP*AP*AP*AP*AP*TP*AP*G)-3'
    ChainsA
    EngineeredYES
    Other DetailsSOLID PHASE DNA SYNTHESIS
    SyntheticYES
 
Molecule 2 - 5'- D(*AP*AP*CP*TP*AP*TP*TP*TP*TP*TP*CP*CP*AP*GP*C)-3'
    ChainsB
    EngineeredYES
    Other DetailsSOLID PHASE DNA SYNTHESIS
    SyntheticYES
 
Molecule 3 - NUCLEAR FACTOR OF ACTIVATED T CELLS 5
    ChainsC, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQE30
    Expression System StrainM15
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentDNA BINDING REGION
    GeneNFAT5
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNF-AT5, TONEBP

 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 1IMH)

(-) Sites  (0, 0)

(no "Site" information available for 1IMH)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1REL_2PS50254 NF-kappa-B/Rel/dorsal domain profile.NFAT5_HUMAN264-443
 
  2C:188-367
D:188-367

(-) Exons   (6, 12)

Asymmetric/Biological Unit (6, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003544361bENSE00001870018chr16:69599887-69600277391NFAT5_HUMAN1-25250--
1.3ENST000003544363ENSE00001679106chr16:69660306-69660431126NFAT5_HUMAN25-67430--
1.5ENST000003544365ENSE00001615344chr16:69680931-69681489559NFAT5_HUMAN67-2531870--
1.6ENST000003544366ENSE00001290443chr16:69687139-69687331193NFAT5_HUMAN253-317652C:188-241
D:188-241
54
54
1.7ENST000003544367ENSE00001319006chr16:69689512-69689702191NFAT5_HUMAN318-381642C:242-305
D:242-305
64
64
1.8ENST000003544368ENSE00001319109chr16:69693630-69693802173NFAT5_HUMAN381-439592C:305-363
D:305-363
59
59
1.9ENST000003544369ENSE00001297928chr16:69703880-69704014135NFAT5_HUMAN439-484462C:363-408
D:363-408
46
46
1.10ENST0000035443610ENSE00001317689chr16:69704139-6970419153NFAT5_HUMAN484-501182C:408-425
D:408-425
18
18
1.11ENST0000035443611ENSE00001296763chr16:69711106-69711238133NFAT5_HUMAN502-546452C:426-468
D:426-468
43
43
1.12aENST0000035443612aENSE00001320052chr16:69718790-6971887384NFAT5_HUMAN546-574290--
1.13ENST0000035443613ENSE00001298766chr16:69724843-69724991149NFAT5_HUMAN574-623500--
1.14ENST0000035443614ENSE00001301675chr16:69725652-697281422491NFAT5_HUMAN624-14548310--
1.15ENST0000035443615ENSE00001389101chr16:69729039-69729282244NFAT5_HUMAN1454-1531780--
1.16bENST0000035443616bENSE00001841643chr16:69730263-697385698307NFAT5_HUMAN-00--

(-) 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:DNA  Length:15
                                                
                1imh A 4001 TTGCTGGAAAAATAG 4015
                                  4010     

Chain B from PDB  Type:DNA  Length:15
                                                
                1imh B 5001 AACTATTTTTCCAGC 5015
                                  5010     

Chain C from PDB  Type:PROTEIN  Length:281
 aligned with NFAT5_HUMAN | O94916 from UniProtKB/Swiss-Prot  Length:1531

    Alignment length:281
                                   273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543 
         NFAT5_HUMAN    264 KKSPMLCGQYPVKSEGKELKIVVQPETQHRARYLTEGSRGSVKDRTQQGFPTVKLEGHNEPVVLQVFVGNDSGRVKPHGFYQACRVTGRNTTPCKEVDIEGTTVIEVGLDPSNNMTLAVDCVGILKLRNADVEARIGIAGSKKKSTRARLVFRVNIMRKDGSTLTLQTPSSPILCTQPAGVPEILKKSLHSCSVKGEEEVFLIGKNFLKGTKVIFQENVSDENSWKSEAEIDMELFHQNHLIVKVPPYHDQHITLPVSVGIYVVTNAGRSHDVQPFTYTPD  544
               SCOP domains d1imhc2 C:188-367 T-cell transcription factor NFAT5 (TONEBP), DNA-binding domain                                                                                                    d1imhc1 C:368-468 T-cell transcription factor NFAT5 (TONEBP)                                          SCOP domains
               CATH domains -----1imhC01 C:193-362  [code=2.60.40.340, no name defined]                                                                                                                    1imhC02 C:363-468 Immunoglobulins                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............ee..eeeeeee........ee..................eeeee.....eeeeeeeee..........eeeee.........eeeee..eeeeeeeehhhhh.eee...eeeee.hhhhhhh............eeeeeeeeeee.....eeeeeee...ee........eeeee...eee.....eeeeeee......eeeee.........eeee..hhhhh...eeeee............eeeeeeeee..ee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE REL_2  PDB: C:188-367 UniProt: 264-443                                                                                                                                              ----------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6  PDB: C:188-241 UniProt: 253-317 [INCOMPLETE]Exon 1.7  PDB: C:242-305 UniProt: 318-381                       ------------------------------------------------------------------------------------------------------Exon 1.10         Exon 1.11  PDB: C:426-468 UniProt: 502-546  Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------Exon 1.8  PDB: C:305-363 UniProt: 381-439                  --------------------------------------------------------------------------------------------------------- Transcript 1 (2)
           Transcript 1 (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: C:363-408 UniProt: 439-484     ------------------------------------------------------------ Transcript 1 (3)
                1imh C  188 KKSPMLCGQYPVKSEGKELKIVVQPETQHRARYLTEGSRGSVKDRTQQGFPTVKLEGHNEPVVLQVFVGNDSGRVKPHGFYQACRVTGRNTTPCKEVDIEGTTVIEVGLDPSNNMTLAVDCVGILKLRNADVEARIGIAGSKKKSTRARLVFRVNIMRKDGSTLTLQTPSSPILCTQPAGVPEILKKSLHSCSVKGEEEVFLIGKNFLKGTKVIFQENVSDENSWKSEAEIDMELFHQNHLIVKVPPYHDQHITLPVSVGIYVVTNAGRSHDVQPFTYTPD  468
                                   197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467 

Chain D from PDB  Type:PROTEIN  Length:281
 aligned with NFAT5_HUMAN | O94916 from UniProtKB/Swiss-Prot  Length:1531

    Alignment length:281
                                   273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543 
         NFAT5_HUMAN    264 KKSPMLCGQYPVKSEGKELKIVVQPETQHRARYLTEGSRGSVKDRTQQGFPTVKLEGHNEPVVLQVFVGNDSGRVKPHGFYQACRVTGRNTTPCKEVDIEGTTVIEVGLDPSNNMTLAVDCVGILKLRNADVEARIGIAGSKKKSTRARLVFRVNIMRKDGSTLTLQTPSSPILCTQPAGVPEILKKSLHSCSVKGEEEVFLIGKNFLKGTKVIFQENVSDENSWKSEAEIDMELFHQNHLIVKVPPYHDQHITLPVSVGIYVVTNAGRSHDVQPFTYTPD  544
               SCOP domains d1imhd2 D:188-367 T-cell transcription factor NFAT5 (TONEBP), DNA-binding domain                                                                                                    d1imhd1 D:368-468 T-cell transcription factor NFAT5 (TONEBP)                                          SCOP domains
               CATH domains -----1imhD01 D:193-362  [code=2.60.40.340, no name defined]                                                                                                                    1imhD02 D:363-468 Immunoglobulins                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............ee..eeeeeee............................eeeee.....eeeeeeeee..........eeeee.........eeeee..eeeeeeeehhhhh.eee...eeeee.hhhhhhhhhh.hhhhh...eeeeeeeeeee.....eeeeeee...ee........eeeee...eee.....eeeeeee......eeeee.........eeee..hhhhh...eeeee............eeeeeeeee..ee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE REL_2  PDB: D:188-367 UniProt: 264-443                                                                                                                                              ----------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6  PDB: D:188-241 UniProt: 253-317 [INCOMPLETE]Exon 1.7  PDB: D:242-305 UniProt: 318-381                       ------------------------------------------------------------------------------------------------------Exon 1.10         Exon 1.11  PDB: D:426-468 UniProt: 502-546  Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------Exon 1.8  PDB: D:305-363 UniProt: 381-439                  --------------------------------------------------------------------------------------------------------- Transcript 1 (2)
           Transcript 1 (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: D:363-408 UniProt: 439-484     ------------------------------------------------------------ Transcript 1 (3)
                1imh D  188 KKSPMLCGQYPVKSEGKELKIVVQPETQHRARYLTEGSRGSVKDRTQQGFPTVKLEGHNEPVVLQVFVGNDSGRVKPHGFYQACRVTGRNTTPCKEVDIEGTTVIEVGLDPSNNMTLAVDCVGILKLRNADVEARIGIAGSKKKSTRARLVFRVNIMRKDGSTLTLQTPSSPILCTQPAGVPEILKKSLHSCSVKGEEEVFLIGKNFLKGTKVIFQENVSDENSWKSEAEIDMELFHQNHLIVKVPPYHDQHITLPVSVGIYVVTNAGRSHDVQPFTYTPD  468
                                   197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467 

   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  (2, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain C,D   (NFAT5_HUMAN | O94916)
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: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:0001816    cytokine production    The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
    GO:0007588    excretion    The elimination by an organism of the waste products that arise as a result of metabolic activity. These products include water, carbon dioxide (CO2), and nitrogenous compounds.
    GO:0010628    positive regulation of gene expression    Any process that increases 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: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:0070884    regulation of calcineurin-NFAT signaling cascade    Any process that modulates the frequency, rate or extent of the calcineurin-NFAT signaling cascade.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006970    response to osmotic stress    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 indicating an increase or decrease in the concentration of solutes outside the organism or cell.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    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: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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