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(-) Description

Title :  STRUCTURE OF THE P22PHOX-P47PHOX COMPLEX
 
Authors :  Y. Groemping, K. Lapouge, S. J. Smerdon, K. Rittinger
Date :  25 Mar 03  (Deposition) - 20 May 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A,B,C,D  (2x)
Keywords :  P47Phox, P22Phox, Nadph Oxidase, Complex, Oxidoreductase Activator (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Groemping, K. Lapouge, S. J. Smerdon, K. Rittinger
Molecular Basis Of Phosphorylation-Induced Activation Of The Nadph Oxidase
Cell(Cambridge, Mass. ) V. 113 343 2003
PubMed-ID: 12732142  |  Reference-DOI: 10.1016/S0092-8674(03)00314-3
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NEUTROPHIL CYTOSOL FACTOR 1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPGEX-6P1
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRESIDUES 156-285
    GeneNCF1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNCF-1, NEUTROPHIL NADPH OXIDASE FACTOR 1, 47 KDA NEUTROPHIL OXIDASE FACTOR, P47-PHOX, NCF-47K, 47 KDA AUTOSOMAL CHRONIC GRANULOMATOUS DISEASE PROTEIN
 
Molecule 2 - FLAVOCYTOCHROME B558 ALPHA POLYPEPTIDE
    ChainsC, D
    EngineeredYES
    FragmentRESIDUES 149-166
    Other DetailsPEPTIDE SYNTHESIS
    SynonymP22 PHAGOCYTE B-CYTOCHROME, NEUTROPHIL CYTOCHROME B, 22 KDA POLYPEPTIDE, P22-PHOX, P22PHOX, CYTOCHROME B558, ALPHA CHAIN, CYTOCHROME B-245 ALPHA-SUBUNIT LIGHT CHAIN, SUPEROXIDE- GENERATING NADPH OXIDASE LIGHT CHAIN SUBUNIT
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)ABCD
Biological Unit 2 (2x)ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1OV3)

(-) Sites  (0, 0)

(no "Site" information available for 1OV3)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1OV3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1OV3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 8)

Asymmetric Unit (4, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_012477T160SNCF1_HUMANPolymorphism  ---A/BT160S
2UniProtVAR_012478N166DNCF1_HUMANPolymorphism4868A/BD166D
3UniProtVAR_018476K258ENCF1_HUMANPolymorphism  ---A/BK258E
4UniProtVAR_012479G262SNCF1_HUMANPolymorphism  ---A/BG262S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (4, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_012477T160SNCF1_HUMANPolymorphism  ---A/BT160S
2UniProtVAR_012478N166DNCF1_HUMANPolymorphism4868A/BD166D
3UniProtVAR_018476K258ENCF1_HUMANPolymorphism  ---A/BK258E
4UniProtVAR_012479G262SNCF1_HUMANPolymorphism  ---A/BG262S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (4, 16)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_012477T160SNCF1_HUMANPolymorphism  ---A/BT160S
2UniProtVAR_012478N166DNCF1_HUMANPolymorphism4868A/BD166D
3UniProtVAR_018476K258ENCF1_HUMANPolymorphism  ---A/BK258E
4UniProtVAR_012479G262SNCF1_HUMANPolymorphism  ---A/BG262S

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

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.NCF1_HUMAN156-215
 
226-285
 
  4A:156-215
B:156-215
A:226-283
B:226-283
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.NCF1_HUMAN156-215
 
226-285
 
  4A:156-215
B:156-215
A:226-283
B:226-283
Biological Unit 2 (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.NCF1_HUMAN156-215
 
226-285
 
  8A:156-215
B:156-215
A:226-283
B:226-283

(-) Exons   (0, 0)

(no "Exon" information available for 1OV3)

(-) Sequences/Alignments

Asymmetric 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:134
 aligned with NCF1_HUMAN | P14598 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:151
                                   142       152       162       172       182       192       202       212       222       232       242       252       262       272       282 
           NCF1_HUMAN   133 TKKPETYLMPKDGKSTATDITGPIILQTYRAIANYEKTSGSEMALSTGDVVEVVEKSESGWWFCQMKAKRGWIPASFLEPLDSPDETEDPEPNYAGEPYVAIKAYTAVEGDEVSLLEGEAVEVIHKLLDGWWVIRKDDVTGYFPSMYLQKS 283
               SCOP domains d1ov3                 a1 A:150-214 p47pox (neutrophil cytosolic factor 1)         d1ov3a2 A:215-283 p47pox (neutrophil cytosolic factor 1)              SCOP domains
               CATH domains --------------------------1ov3A01 A:159-213 SH3 Domains                          ---------------1ov3A02 A:229-283 SH3 Domains                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....-----------------....eeeee..................eeeeeee....eeeeee...eeeee...eee................eeeee..................eeeeee.....eeeeee..eeeeee...eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------S-----D-------------------------------------------------------------------------------------------E---S--------------------- SAPs(SNPs)
                    PROSITE -----------------------SH3  PDB: A:156-215 UniProt: 156-215                        ----------SH3  PDB: A:226-283 UniProt: 226-285                       PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ov3 A 150 LGSPE-----------------FIILQTYRAIADYEKTSGSEMALSTGDVVEVVEKSESGWWFCQMKAKRGWIPASFLEPLDSPDETEDPEPNYAGEPYVAIKAYTAVEGDEVSLLEGEAVEVIHKLLDGWWVIRKDDVTGYFPSMYLQKS 283
                                |    -         -  |    162       172       182       192       202       212       222       232       242       252       262       272       282 
                              154               155                                                                                                                                

Chain B from PDB  Type:PROTEIN  Length:127
 aligned with NCF1_HUMAN | P14598 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:149
                                   144       154       164       174       184       194       204       214       224       234       244       254       264       274         
           NCF1_HUMAN   135 KPETYLMPKDGKSTATDITGPIILQTYRAIANYEKTSGSEMALSTGDVVEVVEKSESGWWFCQMKAKRGWIPASFLEPLDSPDETEDPEPNYAGEPYVAIKAYTAVEGDEVSLLEGEAVEVIHKLLDGWWVIRKDDVTGYFPSMYLQKS 283
               SCOP domains d1ov                 3b1 B:152-214 p47pox (neutrophil cytosolic factor 1)       d1o     v3b2 B:215-283 p47pox (neutrophil cytosolic factor 1)         SCOP domains
               CATH domains ------------------------1ov3B01 B:159-213 SH3 Domains                          ---------------1ov3B02 B:229-283 SH3 Domains                           CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------SH3_1-1ov3B01 B:232-277                       ------ Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------SH3_1-1ov3B02 B:232-277                       ------ Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------------SH3_1-1ov3B03 B:232-277                       ------ Pfam domains (3)
           Pfam domains (4) -------------------------------------------------------------------------------------------------SH3_1-1ov3B04 B:232-277                       ------ Pfam domains (4)
         Sec.struct. author ....-----------------...eeeee..................eeeeeee....eeeeee...eeeee...eee.....-----......eeeee..................eeeeee.....eeeeee..eeeeee...eee. Sec.struct. author
                 SAPs(SNPs) -------------------------S-----D-------------------------------------------------------------------------------------------E---S--------------------- SAPs(SNPs)
                    PROSITE ---------------------SH3  PDB: B:156-215 UniProt: 156-215                        ----------SH3  PDB: B:226-283 UniProt: 226-285                       PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ov3 B 152 SPEF-----------------IILQTYRAIADYEKTSGSEMALSTGDVVEVVEKSESGWWFCQMKAKRGWIPASFLEPLDSPD-----EPNYAGEPYVAIKAYTAVEGDEVSLLEGEAVEVIHKLLDGWWVIRKDDVTGYFPSMYLQKS 283
                               |     -         - |     164       174       184       194       204       214  |    224       234       244       254       264       274         
                             155               156                                                          217   223                                                            

Chain C from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 1ov3 C 150 QPPSNPPPRPP 160
                                   159 

Chain D from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 1ov3 D 150 QPPSNPPPRPP 160
                                   159 

   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 Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
1a1ov3A01A:159-213
1b1ov3B01B:159-213
1c1ov3A02A:229-283
1d1ov3B02B:229-283

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: SH3 (175)
(-)
Family: SH3_1 (141)
1aSH3_1-1ov3B01B:232-277
1bSH3_1-1ov3B02B:232-277
1cSH3_1-1ov3B03B:232-277
1dSH3_1-1ov3B04B:232-277

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NCF1_HUMAN | P14598)
molecular function
    GO:0017124    SH3 domain binding    Interacting selectively and non-covalently with a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins.
    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:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0035091    phosphatidylinositol binding    Interacting selectively and non-covalently with any inositol-containing glycerophospholipid, i.e. phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
    GO:0043325    phosphatidylinositol-3,4-bisphosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-3,4-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' and 4' positions.
    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:0006612    protein targeting to membrane    The process of directing proteins towards a membrane, usually using signals contained within the protein.
    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: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:0019898    extrinsic component of membrane    The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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
        NCF1_HUMAN | P145981gd5 1k4u 1kq6 1ng2 1o7k 1uec 1w70 1wlp

(-) Related Entries Specified in the PDB File

1ng2 STRUCTURE OF AUTOINHIBITED P47PHOX