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- PDB-7yxw: Structure of the p22phox A200G mutant in complex with p47phox peptide -

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Basic information

Entry
Database: PDB / ID: 7yxw
TitleStructure of the p22phox A200G mutant in complex with p47phox peptide
Components
  • Cytochrome b-245 light chain
  • Neutrophil cytosol factor 1
KeywordsOXIDOREDUCTASE / NADPH oxidase complex / oxidoreductase activator
Function / homology
Function and homology information


negative regulation of glomerular filtration by angiotensin / smooth muscle hypertrophy / regulation of respiratory burst involved in inflammatory response / neutrophil-mediated killing of gram-positive bacterium / positive regulation of mucus secretion / superoxide-generating NADPH oxidase activator activity / cellular response to L-glutamine / neutrophil-mediated killing of fungus / phagolysosome / positive regulation of toll-like receptor 2 signaling pathway ...negative regulation of glomerular filtration by angiotensin / smooth muscle hypertrophy / regulation of respiratory burst involved in inflammatory response / neutrophil-mediated killing of gram-positive bacterium / positive regulation of mucus secretion / superoxide-generating NADPH oxidase activator activity / cellular response to L-glutamine / neutrophil-mediated killing of fungus / phagolysosome / positive regulation of toll-like receptor 2 signaling pathway / positive regulation of defense response to bacterium / mucus secretion / perinuclear endoplasmic reticulum / cellular response to testosterone stimulus / Cross-presentation of particulate exogenous antigens (phagosomes) / superoxide-generating NAD(P)H oxidase activity / leukotriene metabolic process / NADPH oxidase complex / cytochrome complex assembly / response to yeast / respiratory burst / WNT5:FZD7-mediated leishmania damping / respiratory burst involved in defense response / cellular response to phorbol 13-acetate 12-myristate / phosphatidylinositol-3,4-bisphosphate binding / ROS and RNS production in phagocytes / response to aldosterone / regulation of release of sequestered calcium ion into cytosol / hydrogen peroxide biosynthetic process / superoxide anion generation / protein targeting to membrane / superoxide metabolic process / Detoxification of Reactive Oxygen Species / positive regulation of reactive oxygen species biosynthetic process / cellular response to angiotensin / tertiary granule membrane / RAC3 GTPase cycle / RAC2 GTPase cycle / RHO GTPases Activate NADPH Oxidases / cellular defense response / specific granule membrane / positive regulation of superoxide anion generation / stress fiber / RAC1 GTPase cycle / positive regulation of endothelial cell proliferation / phosphatidylinositol binding / establishment of localization in cell / epithelial cell proliferation / secretory granule / positive regulation of phagocytosis / positive regulation of smooth muscle cell proliferation / response to interleukin-1 / response to activity / cellular response to mechanical stimulus / cellular response to glucose stimulus / cellular response to gamma radiation / response to nutrient levels / SH3 domain binding / positive regulation of interleukin-6 production / VEGFA-VEGFR2 Pathway / cellular response to tumor necrosis factor / phagocytic vesicle membrane / cytoplasmic side of plasma membrane / positive regulation of tumor necrosis factor production / positive regulation of cell growth / response to hypoxia / electron transfer activity / endosome / apical plasma membrane / response to xenobiotic stimulus / inflammatory response / protein heterodimerization activity / innate immune response / focal adhesion / neuronal cell body / heme binding / Neutrophil degranulation / dendrite / endoplasmic reticulum membrane / membrane / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Cytochrome b558 alpha-subunit / Cytochrome Cytochrome b558 alpha-subunit / 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 ...Cytochrome b558 alpha-subunit / Cytochrome Cytochrome b558 alpha-subunit / 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 / : / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
Cytochrome b-245 light chain / Neutrophil cytosol factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCukier, C.D. / Vuillard, L.M. / Komjati, B. / Szlavik, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Med.Chem.Lett. / Year: 2022
Title: Targeting NOX2 via p47/phox-p22/phox Inhibition with Novel Triproline Mimetics
Authors: Garsi, J.B. / Komjati, B. / Cullia, G. / Fejes, I. / Sipos, M. / Sipos, Z. / Fordos, E. / Markacz, P. / Balazs, B. / Lancelot, N. / Berger, S. / Raimbaud, E. / Brown, D. / Vuillard, L.M. / ...Authors: Garsi, J.B. / Komjati, B. / Cullia, G. / Fejes, I. / Sipos, M. / Sipos, Z. / Fordos, E. / Markacz, P. / Balazs, B. / Lancelot, N. / Berger, S. / Raimbaud, E. / Brown, D. / Vuillard, L.M. / Haberkorn, L. / Cukier, C. / Szlavik, Z. / Hanessian, S.
History
DepositionFeb 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Cytochrome b-245 light chain
A: Neutrophil cytosol factor 1


Theoretical massNumber of molelcules
Total (without water)16,5822
Polymers16,5822
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-10 kcal/mol
Surface area7920 Å2
Unit cell
Length a, b, c (Å)102.444, 102.444, 56.075
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein/peptide Cytochrome b-245 light chain / Cytochrome b(558) alpha chain / Cytochrome b558 subunit alpha / Neutrophil cytochrome b 22 kDa ...Cytochrome b(558) alpha chain / Cytochrome b558 subunit alpha / Neutrophil cytochrome b 22 kDa polypeptide / Superoxide-generating NADPH oxidase light chain subunit / p22 phagocyte B-cytochrome / p22-phox / p22phox


Mass: 1927.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P13498
#2: Protein Neutrophil cytosol factor 1 / NCF-1 / 47 kDa autosomal chronic granulomatous disease protein / 47 kDa neutrophil oxidase factor / ...NCF-1 / 47 kDa autosomal chronic granulomatous disease protein / 47 kDa neutrophil oxidase factor / NCF-47K / Neutrophil NADPH oxidase factor 1 / Nox organizer 2 / Nox-organizing protein 2 / SH3 and PX domain-containing protein 1A / p47-phox


Mass: 14654.306 Da / Num. of mol.: 1 / Mutation: A200G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCF1, NOXO2, SH3PXD1A / Production host: Escherichia coli (E. coli) / References: UniProt: P14598

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 1.2 M sodium citrate tribasic dihydrate, 1:1 protein:precipitant ratio

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.5→45.81 Å / Num. obs: 10811 / % possible obs: 99.9 % / Redundancy: 12 % / Biso Wilson estimate: 58.9 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.031 / Rrim(I) all: 0.104 / Net I/σ(I): 11.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.5-2.612.91.1411525411810.9270.3381.1921.799.9
9.01-45.81100.04828442830.9990.0150.05126.898.7

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Processing

Software
NameVersionClassification
XDSVERSION January 10, 2014data reduction
Aimless0.5.27data scaling
REFMAC5.8.0151refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ng2

1ng2


Resolution: 2.5→40 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.931 / SU B: 16.798 / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.265 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2686 554 5.1 %RANDOM
Rwork0.2411 ---
obs0.2426 10220 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 189.26 Å2 / Biso mean: 91.471 Å2 / Biso min: 60.34 Å2
Baniso -1Baniso -2Baniso -3
1--9.77 Å20 Å20 Å2
2---9.77 Å20 Å2
3---19.55 Å2
Refinement stepCycle: final / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1093 0 0 0 1093
Num. residues----139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021126
X-RAY DIFFRACTIONr_bond_other_d0.0020.021027
X-RAY DIFFRACTIONr_angle_refined_deg1.8111.9721537
X-RAY DIFFRACTIONr_angle_other_deg1.05132395
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6085137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg47.01325.10249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.90515177
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.307154
X-RAY DIFFRACTIONr_chiral_restr0.10.2162
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211251
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02227
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 37 -
Rwork0.529 733 -
all-770 -
obs--99.87 %

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