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(-) Description

Title :  REFINED SOLUTION STRUCTURE OF THE 1ST SH3 DOMAIN FROM HUMAN NEUTROPHIL CYTOSOL FACTOR 2 (NCF-2)
 
Authors :  N. Tochio, E. Chikayama, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  22 Apr 06  (Deposition) - 02 May 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Sh3 Domain, Neutrophil Cytosol Factor, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Tochio, E. Chikayama, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The 1St Sh3 Domain From Human Neutrophil Cytosol Factor 2 (Ncf-2)
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NEUTROPHIL CYTOSOL FACTOR 2
    ChainsA
    EngineeredYES
    Expression System PlasmidP040921-05
    Expression System Vector TypePLASMID
    FragmentSH3 DOMAIN
    GeneNCF2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymNCF-2, NEUTROPHIL NADPH OXIDASE FACTOR 2, 67 KDA NEUTROPHIL OXIDASE FACTOR, P67-PHOX, NOXA2

 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 2DMO)

(-) Sites  (0, 0)

(no "Site" information available for 2DMO)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

NMR Structure (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_034129T279MNCF2_HUMANPolymorphism13306581AT44M
2UniProtVAR_034130V297ANCF2_HUMANPolymorphism35937854AV62A

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.NCF2_HUMAN240-299
457-516
  1A:7-62
-

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003675361ENSE00001444961chr1:183560011-18355997537NCF2_HUMAN-00--
1.2cENST000003675362cENSE00001444960chr1:183559494-183559291204NCF2_HUMAN1-58580--
1.3ENST000003675363ENSE00000774250chr1:183556112-18355603083NCF2_HUMAN59-86280--
1.4ENST000003675364ENSE00000922163chr1:183546842-183546734109NCF2_HUMAN86-122370--
1.5ENST000003675365ENSE00000922162chr1:183543756-183543622135NCF2_HUMAN123-167450--
1.6ENST000003675366ENSE00000922161chr1:183542427-183542320108NCF2_HUMAN168-203360--
1.7aENST000003675367aENSE00000922160chr1:183539974-18353991560NCF2_HUMAN204-223201A:1-66
1.8bENST000003675368bENSE00000774245chr1:183538320-18353827744NCF2_HUMAN224-238150--
1.9bENST000003675369bENSE00001592444chr1:183536480-183536339142NCF2_HUMAN238-285481A:7-5044
1.10ENST0000036753610ENSE00000774243chr1:183536123-18353605569NCF2_HUMAN286-308231A:51-6414
1.11ENST0000036753611ENSE00001738087chr1:183534914-18353483976NCF2_HUMAN309-334261A:65-68 (gaps)7
1.12bENST0000036753612bENSE00001735809chr1:183533165-18353314026NCF2_HUMAN334-34290--
1.12cENST0000036753612cENSE00001784834chr1:183532720-183532569152NCF2_HUMAN343-393510--
1.13cENST0000036753613cENSE00000922153chr1:183532441-183532330112NCF2_HUMAN393-430380--
1.14bENST0000036753614bENSE00000774239chr1:183529408-183529231178NCF2_HUMAN431-490600--
1.15bENST0000036753615bENSE00001444959chr1:183525365-183524698668NCF2_HUMAN490-526370--

(-) 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:68
 aligned with NCF2_HUMAN | P19878 from UniProtKB/Swiss-Prot  Length:526

    Alignment length:115
                                   222       232       242       252       262       272       282       292       302       312       322     
           NCF2_HUMAN   213 SFSGFAPLQPQAAEPPPRPKTPEIFRALEGEAHRVLFGFVPETKEELQVMPGNIVFVLKKGNDNWATVMFNGQKGLVPCNYLEPVELRIHPQQQPQEESSPQSDIPAPPSSKAPG 327
               SCOP domains d2dmoa                       _ A: p67phox                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......-----------------------.eeeee..................eeee.ee.....eeeee..eeeee....eee...---------------------...---. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------M-----------------A------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------SH3  PDB: A:7-62 UniProt: 240-299                           ---------------------------- PROSITE
           Transcript 1 (1) Exon 1.7a  Exon 1.8b      -----------------------------------------------Exon 1.10  PDB: A:51-64Exon 1.11           Transcript 1 (1)
           Transcript 1 (2) -------------------------Exon 1.9b  PDB: A:7-50 UniProt: 238-285         ------------------------------------------ Transcript 1 (2)
                 2dmo A   1 GSSGSS-----------------------GEAHRVLFGFVPETKEELQVMPGNIVFVLKKGNDNWATVMFNGQKGLVPCNYLEPVSG---------------------PSS---G  68
                                 |   -         -         7        17        27        37        47        57      |  -         -        66|   |
                                 6                       7                                                       64                    65 |  68
                                                                                                                                         67    

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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, 1)

NMR Structure

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 20)

NMR Structure(hide GO term definitions)
Chain A   (NCF2_HUMAN | P19878)
molecular function
    GO:0048365    Rac GTPase binding    Interacting selectively and non-covalently with Rac protein, any member of the Rac subfamily of the Ras superfamily of monomeric GTPases.
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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:0016175    superoxide-generating NADPH oxidase activity    Catalysis of the reaction: NAD(P)H + O2 = NAD(P)H + O2-.
biological process
    GO:0002479    antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent    The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class I protein complex following intracellular transport via a TAP (transporter associated with antigen processing) pathway. The peptide is typically a fragment of a larger exogenous protein which has been degraded within the cell and is dependent on TAP transport from the cytosol to ER for association with the MHC class I molecule. Class I here refers to classical class I molecules.
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    GO:0006968    cellular defense response    A defense response that is mediated by cells.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0045730    respiratory burst    A phase of elevated metabolic activity, during which oxygen consumption increases; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals.
    GO:0042554    superoxide anion generation    The enzymatic generation of superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species, by a cell in response to environmental stress, thereby mediating the activation of various stress-inducible signaling pathways.
    GO:0006801    superoxide metabolic process    The chemical reactions and pathways involving superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species.
    GO:0048010    vascular endothelial growth factor receptor signaling pathway    Any series of molecular signals initiated by the binding of an extracellular ligand to a vascular endothelial growth factor receptor (VEGFR) located on the surface of the receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    GO:0043020    NADPH oxidase complex    A enzyme complex of which the core is a heterodimer composed of a light (alpha) and heavy (beta) chain, and requires several other water-soluble proteins of cytosolic origin for activity. Functions in superoxide generation by the NADPH-dependent reduction of O2.
    GO:0001669    acrosomal vesicle    A structure in the head of a spermatozoon that contains acid hydrolases, and is concerned with the breakdown of the outer membrane of the ovum during fertilization. It lies just beneath the plasma membrane and is derived from the lysosome.
    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:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0032010    phagolysosome    A membrane-bounded intracellular vesicle formed by maturation of an early phagosome following the ingestion of particulate material by phagocytosis; during maturation, phagosomes acquire markers of late endosomes and lysosomes.

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 Related Entries

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

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        NCF2_HUMAN | P198781e96 1hh8 1k4u 1oey 1wm5

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