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- PDB-1k4u: Solution structure of the C-terminal SH3 domain of p67phox comple... -

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Basic information

Entry
Database: PDB / ID: 1k4u
TitleSolution structure of the C-terminal SH3 domain of p67phox complexed with the C-terminal tail region of p47phox
Components
  • PHAGOCYTE NADPH OXIDASE SUBUNIT P47PHOX
  • PHAGOCYTE NADPH OXIDASE SUBUNIT P67PHOX
KeywordsHORMONE/GROWTH FACTOR / P67PHOX / P47PHOX / SH3-PEPTIDE COMPLEX / HELIX-TURN-HELIX / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


reactive oxygen species biosynthetic process / regulation of respiratory burst involved in inflammatory response / superoxide-generating NADPH oxidase activator activity / superoxide-generating NAD(P)H oxidase activity / phagolysosome / positive regulation of epidermal growth factor-activated receptor activity / Cross-presentation of particulate exogenous antigens (phagosomes) / NADPH oxidase complex / respiratory burst / cellular response to testosterone stimulus ...reactive oxygen species biosynthetic process / regulation of respiratory burst involved in inflammatory response / superoxide-generating NADPH oxidase activator activity / superoxide-generating NAD(P)H oxidase activity / phagolysosome / positive regulation of epidermal growth factor-activated receptor activity / Cross-presentation of particulate exogenous antigens (phagosomes) / NADPH oxidase complex / respiratory burst / cellular response to testosterone stimulus / ROS and RNS production in phagocytes / phosphatidylinositol-3,4-bisphosphate binding / superoxide anion generation / protein targeting to membrane / positive regulation of p38MAPK cascade / superoxide metabolic process / Detoxification of Reactive Oxygen Species / RHO GTPases Activate NADPH Oxidases / RAC3 GTPase cycle / RAC2 GTPase cycle / cellular defense response / phagocytosis / cellular response to cadmium ion / RAC1 GTPase cycle / phosphatidylinositol binding / acrosomal vesicle / cellular response to glucose stimulus / positive regulation of JNK cascade / cytoplasmic side of plasma membrane / small GTPase binding / SH3 domain binding / cellular response to reactive oxygen species / VEGFA-VEGFR2 Pathway / electron transfer activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / innate immune response / dendrite / neuronal cell body / positive regulation of DNA-templated transcription / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Neutrophil cytosol factor 2, PB1 domain / Neutrophil cytosol factor 2 / Neutrophil cytosol factor 2, SH3 domain 1 / Neutrophil cytosol factor 1 / Neutrophil cytosol factor 1, C-terminal / Neutrophil cytosol factor 1, PBR/AIR / Neutrophil cytosol factor 1, PX domain / Neutrophil cytosol factor 1, first SH3 domain / Neutrophil cytosol factor 1, second SH3 domain / NADPH oxidase subunit p47Phox, C terminal domain ...Neutrophil cytosol factor 2, PB1 domain / Neutrophil cytosol factor 2 / Neutrophil cytosol factor 2, SH3 domain 1 / Neutrophil cytosol factor 1 / Neutrophil cytosol factor 1, C-terminal / Neutrophil cytosol factor 1, PBR/AIR / Neutrophil cytosol factor 1, PX domain / Neutrophil cytosol factor 1, first SH3 domain / Neutrophil cytosol factor 1, second SH3 domain / NADPH oxidase subunit p47Phox, C terminal domain / Neutrophil cytosol factor 1, PBR/AIR / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / Tetratricopeptide repeat / SH3 Domains / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / SH3 domain / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tetratricopeptide-like helical domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Neutrophil cytosol factor 1 / Neutrophil cytosol factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsKami, K. / Takeya, R. / Sumimoto, H. / Kohda, D.
CitationJournal: EMBO J. / Year: 2002
Title: Diverse recognition of non-PxxP peptide ligands by the SH3 domains from p67(phox), Grb2 and Pex13p.
Authors: Kami, K. / Takeya, R. / Sumimoto, H. / Kohda, D.
History
DepositionOct 8, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
S: PHAGOCYTE NADPH OXIDASE SUBUNIT P67PHOX
P: PHAGOCYTE NADPH OXIDASE SUBUNIT P47PHOX


Theoretical massNumber of molelcules
Total (without water)10,3622
Polymers10,3622
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)22 / 100structures with the lowest energy
RepresentativeModel #7lowest energy

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Components

#1: Protein PHAGOCYTE NADPH OXIDASE SUBUNIT P67PHOX / Neutrophil cytosol factor 2


Mass: 6937.713 Da / Num. of mol.: 1 / Fragment: C-TERMINAL SH3 DOMAIN (RESIDUES 455-516) / Mutation: C499S/C514S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCF2 / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P19878
#2: Protein/peptide PHAGOCYTE NADPH OXIDASE SUBUNIT P47PHOX / Neutrophil cytosol factor 1


Mass: 3423.983 Da / Num. of mol.: 1 / Fragment: TAIL PEPTIDE (RESIDUES 359-390)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCF1 / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P14598

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCA, HN(CO)CA, CBCA(CO)NH, HN(CA)CB, HBHA(CO)NH, (H)CCH-COSY, (H)CCH-TOCSY, CCH-COSY, 15N-RESOLVED NOESY, 15-RESOLVED TOCSY, HNHA, HNHB, 3D F1 13C-FILTERED-F3 13C-RESOLVED NOESY, 3D F1 15N-FILTERED-F3 15N-RESOLVED NOESY, 2D SPIN-ECHO DIFFERENCE EXPERIMENTS
122HNCA, HN(CO)CA, CBCA(CO)NH, HN(CA)CB, HBHA(CO)NH, (H)CCH-COSY, (H)CCH-TOCSY, CCH-COSY, 15N-RESOLVED NOESY, 15-RESOLVED TOCSY, HNHA, HNHB, 3D F1 13C-FILTERED-F3 13C-RESOLVED NOESY, 3D F1 15N-FILTERED-F3 15N-RESOLVED NOESY, 2D SPIN-ECHO DIFFERENCE EXPERIMENTS

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7mM p67SH3(C) U-15N,13C; 0.77mM p47 tail peptide; 5mM MOPSO buffer; 30 mM d10-DTT; 100mM KCl90% H2O, 10% D2O; 100% D2O
20.5mM p47 tail peptide U-15N,13C; 0.55mM p67SH3(C); 5mM MOPSO buffer; 30mM d10-DTT; 100mM KCl90% H2O, 10% D2O; 100% D2O
Sample conditionsIonic strength: 100mM KCl / pH: 7.1 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker DMXBrukerDMX7502

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Processing

NMR software
NameVersionDeveloperClassification
CNS1Brungerstructure solution
CNS1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 693 restraints, 611 are NOE-derived distance constraints, 82 dihedral angle restraints. No hydrogen bond restraint was used.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 22

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