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(-) Description

Title :  SOLUTION STRUCTURE OF THE DEATH DOMAIN OF NUCLEAR FACTOR NF-KAPPA-B P100
 
Authors :  T. Nagashima, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  08 Dec 05  (Deposition) - 08 Dec 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Six Helix Bundle, Processing, Proteasome, Signal Transduction, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Nagashima, F. Hayashi, S. Yokoyama
Solution Structure Of The Death Domain Of Nuclear Factor Nf-Kappa-B P100
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NUCLEAR FACTOR NF-KAPPA-B P100 SUBUNIT
    ChainsA
    EngineeredYES
    Expression System PlasmidP050404-15
    Expression System Vector TypePLASMID
    FragmentDEATH DOMAIN
    GeneNFKB2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2D96)

(-) Sites  (0, 0)

(no "Site" information available for 2D96)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2D96)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2D96)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D96)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2D96)

(-) Exons   (5, 5)

NMR Structure (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003699661bENSE00001451363chr10:104154354-104154531178NFKB2_HUMAN-00--
1.2dENST000003699662dENSE00002189547chr10:104155645-10415573793NFKB2_HUMAN1-770--
1.3ENST000003699663ENSE00001377720chr10:104156010-10415609182NFKB2_HUMAN8-35280--
1.4ENST000003699664ENSE00000811509chr10:104156206-10415624641NFKB2_HUMAN35-48140--
1.5bENST000003699665bENSE00000811510chr10:104156482-10415658099NFKB2_HUMAN49-81330--
1.6ENST000003699666ENSE00000503288chr10:104156661-104156812152NFKB2_HUMAN82-132510--
1.7ENST000003699667ENSE00000811512chr10:104157059-104157165107NFKB2_HUMAN132-168370--
1.8ENST000003699668ENSE00000811513chr10:104157284-104157442159NFKB2_HUMAN168-221540--
1.9ENST000003699669ENSE00000811514chr10:104157738-104157842105NFKB2_HUMAN221-256360--
1.10ENST0000036996610ENSE00000811515chr10:104157969-10415805486NFKB2_HUMAN256-284290--
1.11ENST0000036996611ENSE00000811516chr10:104158142-104158280139NFKB2_HUMAN285-331470--
1.12aENST0000036996612aENSE00000503294chr10:104158496-104158621126NFKB2_HUMAN331-373430--
1.13ENST0000036996613ENSE00000722725chr10:104159045-104159254210NFKB2_HUMAN373-443710--
1.14ENST0000036996614ENSE00001192756chr10:104159334-104159475142NFKB2_HUMAN443-490480--
1.15ENST0000036996615ENSE00000722730chr10:104159837-104159951115NFKB2_HUMAN490-528390--
1.16ENST0000036996616ENSE00000722731chr10:104160035-104160248214NFKB2_HUMAN529-600720--
1.17bENST0000036996617bENSE00000722732chr10:104160412-104160581170NFKB2_HUMAN600-656570--
1.18aENST0000036996618aENSE00000722733chr10:104160704-104160806103NFKB2_HUMAN657-691350--
1.18cENST0000036996618cENSE00000722734chr10:104160937-104161088152NFKB2_HUMAN691-741511A:1-55
1.19ENST0000036996619ENSE00000722737chr10:104161206-10416127570NFKB2_HUMAN742-765241A:6-72
1.20ENST0000036996620ENSE00000722739chr10:104161502-104161674173NFKB2_HUMAN765-822581A:7-6458
1.21ENST0000036996621ENSE00000722741chr10:104161805-104161916112NFKB2_HUMAN823-860381A:65-10137
1.22bENST0000036996622bENSE00001192799chr10:104162009-104162281273NFKB2_HUMAN860-900411A:102-109 (gaps)28

(-) Sequences/Alignments

NMR Structure
   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:109
 aligned with NFKB2_HUMAN | Q00653 from UniProtKB/Swiss-Prot  Length:900

    Alignment length:173
                                   725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885   
          NFKB2_HUMAN   716 DSEGPEKDTRSSFRGHTPLDLTCSTKVKTLLLNAAQNTMEPPLTPPSPAGPGLSLGDTALQNLEQLLDGPEAQGSWAELAERLGLRSLVDTYRQTTSPSGSLLRSYELAGGDLAGLLEALSDMGLEEGVRLLRGPETRDKLPSTAEVKEDSAYGSQSVEQEAEKLGPPPEPPG 888
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....-------------------------------------------.......hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..........-...-----------------...---.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.18c  PDB: A:1-5    Exon 1.19  PDB: A:6-7   ---------------------------------------------------------Exon 1.21  PDB: A:65-101 [INCOMPLETE] ---------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------Exon 1.20  PDB: A:7-64 UniProt: 765-822                   -------------------------------------Exon 1.22b UniProt: 860-900   Transcript 1 (2)
                 2d96 A   1 GSSGS-------------------------------------------SGPGLSLGDTALQNLEQLLDGPEAQGSWAELAERLGLRSLVDTYRQTTSPSGSLLRSYELAGGDLAGLLEALSDMGLEEGVRLLRGPETRDKLPST-EVS-----------------GPS---SG 109
                                |    -         -         -         -        |7        17        27        37        47        57        67        77        87        97   | | | -         -     | | - | 
                                5                                           6                                                                                            101 | |               105 | 108 
                                                                                                                                                                           102 |                 107     
                                                                                                                                                                             104                         

   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  (0, 0)

(no "SCOP Domain" information available for 2D96)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2D96)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D96)

(-) Gene Ontology  (33, 33)

NMR Structure(hide GO term definitions)
Chain A   (NFKB2_HUMAN | Q00653)
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:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    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:0003713    transcription coactivator activity    Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating 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: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:0007249    I-kappaB kinase/NF-kappaB signaling    The process in which a signal is passed on to downstream components within the cell through the I-kappaB-kinase (IKK)-dependent activation of NF-kappaB. The cascade begins with activation of a trimeric IKK complex (consisting of catalytic kinase subunits IKKalpha and/or IKKbeta, and the regulatory scaffold protein NEMO) and ends with the regulation of transcription of target genes by NF-kappaB. In a resting state, NF-kappaB dimers are bound to I-kappaB proteins, sequestering NF-kappaB in the cytoplasm. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing the NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription.
    GO:0038061    NIK/NF-kappaB signaling    The process in which a signal is passed on to downstream components within the cell through the NIK-dependent processing and activation of NF-KappaB. Begins with activation of the NF-KappaB-inducing kinase (NIK), which in turn phosphorylates and activates IkappaB kinase alpha (IKKalpha). IKKalpha phosphorylates the NF-Kappa B2 protein (p100) leading to p100 processing and release of an active NF-KappaB (p52).
    GO:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    GO:0030198    extracellular matrix organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
    GO:0002268    follicular dendritic cell differentiation    The process in which a relatively unspecialized precursor cell acquires the specialized features of a follicular dendritic cell.
    GO:0002467    germinal center formation    The process in which germinal centers form. A germinal center is a specialized microenvironment formed when activated B cells enter lymphoid follicles. Germinal centers are the foci for B cell proliferation and somatic hypermutation.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    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:0051092    positive regulation of NF-kappaB transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
    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: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:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates 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:0034097    response to cytokine    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 cytokine 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:0048511    rhythmic process    Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
    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:0048536    spleen development    The process whose specific outcome is the progression of the spleen over time, from its formation to the mature structure. The spleen is a large vascular lymphatic organ composed of white and red pulp, involved both in hemopoietic and immune system functions.
    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:0033257    Bcl3/NF-kappaB2 complex    A protein complex containing one Bcl protein and one or more copies of NF-kappaB2; formation of complexes of different stoichiometry depends on the Bcl3:NF-kappaB2 ratio, and allow Bcl3 to exert different regulatory effects on NF-kappaB2-dependent transcription.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NFKB2_HUMAN | Q006531a3q 3do7 4ot9

(-) Related Entries Specified in the PDB File

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