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(-) Description

Title :  THE ACTIVE N-TERMINAL REGION OF P67PHOX: STRUCTURE AT 1.8 ANGSTROM RESOLUTION AND BIOCHEMICAL CHARACTERIZATIONS OF THE A128V MUTANT IMPLICATED IN CHRONIC GRANULOMATOUS DISEASE
 
Authors :  S. Grizot, F. Fieschi, M. -C. Dagher, E. Pebay-Peyroula
Date :  21 Dec 00  (Deposition) - 13 Jun 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Cell Cycle, Phagocyte Oxidase Factor, Sh3 Domain, Repeat, Tpr Repeat Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Grizot, F. Fieschi, M. -C. Dagher, E. Pebay-Peyroula
The Active N-Terminal Region Of P67Phox: Structure At 1. 8 Angstrom Resolution And Biochemical Characterizations Of The A128V Mutant Implicated In Chronic Granulomatous Disease
J. Biol. Chem. V. 276 21627 2001
PubMed-ID: 11262407  |  Reference-DOI: 10.1074/JBC.M100893200

(-) Compounds

Molecule 1 - NEUTROPHIL CYTOSOL FACTOR 2
    CellNEUTROPHIL
    Cellular LocationCYTOPLASM
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-15B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL DOMAIN, RESIDUES 1-213
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymP67PHOX, NCF-2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1FLC1Ligand/IonCITRATE ANION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:6 , ILE A:7 , TRP A:10 , PRO A:35 , HIS A:36 , ARG A:38 , ILE A:39 , LYS A:138 , GLU A:141 , GLU A:142 , HOH A:2158 , HOH A:2159 , HOH A:2160BINDING SITE FOR RESIDUE FLC A1201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1HH8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1HH8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (15, 15)

Asymmetric/Biological Unit (15, 15)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_065002N42SNCF2_HUMANDisease (CGD2)137854514AN42S
02UniProtVAR_065003G44CNCF2_HUMANDisease (CGD2)137854510AG44C
03UniProtVAR_065004G44RNCF2_HUMANDisease (CGD2)137854510AG44R
04UniProtVAR_017388R77QNCF2_HUMANDisease (CGD2)119103275AR77Q
05UniProtVAR_008904G78ENCF2_HUMANDisease (CGD2)137854519AG78E
06UniProtVAR_065006M79VNCF2_HUMANPolymorphism137854512AM79V
07UniProtVAR_065007D93ENCF2_HUMANDisease (CGD2)137854507AD93E
08UniProtVAR_065009R102PNCF2_HUMANDisease (CGD2)137854515AR102P
09UniProtVAR_065010D108VNCF2_HUMANDisease (CGD2)137854509AD108V
10UniProtVAR_017389A128VNCF2_HUMANDisease (CGD2)119103274AA128V
11UniProtVAR_065011W137RNCF2_HUMANDisease (CGD2)137854516AW137R
12UniProtVAR_065012A140DNCF2_HUMANDisease (CGD2)137854520AA140D
13UniProtVAR_065013Q169ENCF2_HUMANDisease (CGD2)137854517AQ169E
14UniProtVAR_018477K181RNCF2_HUMANPolymorphism2274064AR181R
15UniProtVAR_065014R184PNCF2_HUMANDisease (CGD2)137854518AR184P

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TPRPS50005 TPR repeat profile.NCF2_HUMAN37-70
71-104
121-154
  3A:37-70
A:71-104
A:121-154
2TPR_REGIONPS50293 TPR repeat region circular profile.NCF2_HUMAN37-104  1A:37-104

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003675361ENSE00001444961chr1:183560011-18355997537NCF2_HUMAN-00--
1.2cENST000003675362cENSE00001444960chr1:183559494-183559291204NCF2_HUMAN1-58581A:2-5857
1.3ENST000003675363ENSE00000774250chr1:183556112-18355603083NCF2_HUMAN59-86281A:59-8628
1.4ENST000003675364ENSE00000922163chr1:183546842-183546734109NCF2_HUMAN86-122371A:86-12237
1.5ENST000003675365ENSE00000922162chr1:183543756-183543622135NCF2_HUMAN123-167451A:123-16745
1.6ENST000003675366ENSE00000922161chr1:183542427-183542320108NCF2_HUMAN168-203361A:168-19326
1.7aENST000003675367aENSE00000922160chr1:183539974-18353991560NCF2_HUMAN204-223200--
1.8bENST000003675368bENSE00000774245chr1:183538320-18353827744NCF2_HUMAN224-238150--
1.9bENST000003675369bENSE00001592444chr1:183536480-183536339142NCF2_HUMAN238-285480--
1.10ENST0000036753610ENSE00000774243chr1:183536123-18353605569NCF2_HUMAN286-308230--
1.11ENST0000036753611ENSE00001738087chr1:183534914-18353483976NCF2_HUMAN309-334260--
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

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:192
 aligned with NCF2_HUMAN | P19878 from UniProtKB/Swiss-Prot  Length:526

    Alignment length:192
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191  
           NCF2_HUMAN     2 SLVEAISLWNEGVLAADKKDWKGALDAFSAVQDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKHLAVAYFQRGMLYYQTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKSEPRHSKIDKAMECVWKQKLYEPVVIPVGKLFRPNERQVAQL 193
               SCOP domains d1hh8a_ A: Neutrophil cytosolic factor 2 (NCF-2, p67-phox)                                                                                                                                       SCOP domains
               CATH domains 1hh8A00 A:2-193  [code=1.25.40.10, no name defined]                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh.hhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....eee.hhhh...eeehhhhhhhhhhhhhhh.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.................hhhhhhh. Sec.struct. author
             SAPs(SNPs) (1) ----------------------------------------S-C--------------------------------QEV-------------E--------P-----V-------------------V--------R--D----------------------------E-----------R--P--------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------------R----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                PROSITE (1) -----------------------------------TPR_REGION  PDB: A:37-104 UniProt: 37-104                           ----------------TPR  PDB: A:121-154               --------------------------------------- PROSITE (1)
                PROSITE (2) -----------------------------------TPR  PDB: A:37-70 UniProt: 37-70  TPR  PDB: A:71-104 UniProt: 71-104----------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2c  PDB: A:2-58 UniProt: 1-58 [INCOMPLETE]        Exon 1.3  PDB: A:59-86      ------------------------------------Exon 1.5  PDB: A:123-167 UniProt: 123-167    Exon 1.6  PDB: A:168-193   Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------Exon 1.4  PDB: A:86-122              ----------------------------------------------------------------------- Transcript 1 (2)
                 1hh8 A   2 SLVEAISLWNEGVLAADKKDWKGALDAFSAVQDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKHLAVAYFQRGMLYYQTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKSEPRHSKIDKAMECVWKQKLYEPVVIPVGRLFRPNERQVAQL 193
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191  

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HH8)

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(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)

UniProtKB/Swiss-Prot
        NCF2_HUMAN | P198781e96 1k4u 1oey 1wm5 2dmo

(-) Related Entries Specified in the PDB File

1e96 STRUCTURE OF THE RAC/P67PHOX COMPLEX