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- PDB-1ov3: Structure of the p22phox-p47phox complex -

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Basic information

Entry
Database: PDB / ID: 1ov3
TitleStructure of the p22phox-p47phox complex
Components
  • Flavocytochrome b558 alpha polypeptide
  • Neutrophil cytosol factor 1
KeywordsOxidoreductase activator / p47phox / p22phox / NADPH oxidase / complex
Function / homology
Function and homology information


regulation of respiratory burst involved in inflammatory response / neutrophil-mediated killing of gram-positive bacterium / superoxide-generating NADPH oxidase activator activity / neutrophil-mediated killing of fungus / phagolysosome / superoxide-generating NAD(P)H oxidase activity / leukotriene metabolic process / Cross-presentation of particulate exogenous antigens (phagosomes) / NADPH oxidase complex / response to yeast ...regulation of respiratory burst involved in inflammatory response / neutrophil-mediated killing of gram-positive bacterium / superoxide-generating NADPH oxidase activator activity / neutrophil-mediated killing of fungus / phagolysosome / superoxide-generating NAD(P)H oxidase activity / leukotriene metabolic process / Cross-presentation of particulate exogenous antigens (phagosomes) / NADPH oxidase complex / response to yeast / cellular response to testosterone stimulus / respiratory burst / respiratory burst involved in defense response / phosphatidylinositol-3,4-bisphosphate binding / ROS and RNS production in phagocytes / hydrogen peroxide biosynthetic process / superoxide anion generation / protein targeting to membrane / superoxide metabolic process / Detoxification of Reactive Oxygen Species / RHO GTPases Activate NADPH Oxidases / RAC2 GTPase cycle / RAC3 GTPase cycle / cellular defense response / RAC1 GTPase cycle / phosphatidylinositol binding / epithelial cell proliferation / cellular response to glucose stimulus / SH3 domain binding / VEGFA-VEGFR2 Pathway / cytoplasmic side of plasma membrane / electron transfer activity / inflammatory response / innate immune response / neuronal cell body / dendrite / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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. ...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 Domains / SH3 domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
: / Neutrophil cytosol factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGroemping, Y. / Lapouge, K. / Smerdon, S.J. / Rittinger, K.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2003
Title: Molecular basis of phosphorylation-induced activation of the NADPH oxidase
Authors: Groemping, Y. / Lapouge, K. / Smerdon, S.J. / Rittinger, K.
History
DepositionMar 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 300Biomolecule: The biologically active unit of p47phox is generated using amino acids 156-200 from ...Biomolecule: The biologically active unit of p47phox is generated using amino acids 156-200 from chain A and amino acids 201-285 from chain B.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neutrophil cytosol factor 1
B: Neutrophil cytosol factor 1
C: Flavocytochrome b558 alpha polypeptide
D: Flavocytochrome b558 alpha polypeptide


Theoretical massNumber of molelcules
Total (without water)34,7934
Polymers34,7934
Non-polymers00
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8270 Å2
ΔGint-67 kcal/mol
Surface area15680 Å2
MethodPISA
2
A: Neutrophil cytosol factor 1
B: Neutrophil cytosol factor 1
C: Flavocytochrome b558 alpha polypeptide
D: Flavocytochrome b558 alpha polypeptide

A: Neutrophil cytosol factor 1
B: Neutrophil cytosol factor 1
C: Flavocytochrome b558 alpha polypeptide
D: Flavocytochrome b558 alpha polypeptide


Theoretical massNumber of molelcules
Total (without water)69,5868
Polymers69,5868
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
Buried area19020 Å2
ΔGint-138 kcal/mol
Surface area28880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.66, 57.81, 45.17
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-350-

HOH

DetailsThe biologically active monomeric unit of p47phox is generated using amino acids 156-200 from chain A and amino acids 201-285 from chain B.

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Components

#1: Protein Neutrophil cytosol factor 1 / NCF-1 / Neutrophil NADPH oxidase factor 1 / 47 kDa neutrophil oxidase factor / p47-phox / NCF-47K / ...NCF-1 / Neutrophil NADPH oxidase factor 1 / 47 kDa neutrophil oxidase factor / p47-phox / NCF-47K / 47 kDa autosomal chronic granulomatous disease protein


Mass: 15396.137 Da / Num. of mol.: 2 / Fragment: Residues 156-285
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCF1 / Plasmid: pGEX-6P1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P14598
#2: Protein/peptide Flavocytochrome b558 alpha polypeptide / p22 phagocyte B-cytochrome / Neutrophil cytochrome B / 22 kDa polypeptide / p22-phox / p22phox / ...p22 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


Mass: 2000.325 Da / Num. of mol.: 2 / Fragment: Residues 149-166 / Source method: obtained synthetically / Details: peptide synthesis / References: GenBank: 4557505
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O

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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: 2.49 Å3/Da / Density % sol: 50.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1 M Na-Citrate, 0.1 M Na-cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120-35 mg/mlprotein1drop
220 mMHEPES1droppH7.0
3100 mM1dropNaCl
42 mMdithiothreitol1drop
512 %PEG30001reservoir
6sodium citrate1reservoirpH5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 3, 2002 / Details: Mirrors
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 226852 / Num. obs: 225037 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.05
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.6 / Num. unique all: 3197 / % possible all: 99.1
Reflection
*PLUS
Lowest resolution: 20 Å / Rmerge(I) obs: 0.05

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NG2

1ng2


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.91 / SU B: 3.342 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1647 5.1 %RANDOM
Rwork0.229 ---
all0.232 31232 --
obs0.232 30873 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.218 Å2
Baniso -1Baniso -2Baniso -3
1--2.15 Å20 Å20 Å2
2--5.08 Å20 Å2
3----2.93 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2221 0 0 207 2428
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222293
X-RAY DIFFRACTIONr_angle_refined_deg1.2581.9643130
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.713278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.72815421
X-RAY DIFFRACTIONr_chiral_restr0.0860.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021776
X-RAY DIFFRACTIONr_nbd_refined0.2350.3977
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.5278
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.361
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2930.520
X-RAY DIFFRACTIONr_mcbond_it0.6791.51420
X-RAY DIFFRACTIONr_mcangle_it1.18122303
X-RAY DIFFRACTIONr_scbond_it1.5923873
X-RAY DIFFRACTIONr_scangle_it2.454.5827
LS refinement shellResolution: 1.802→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.329 103
Rwork0.279 2117
obs-2117
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.09880.9313-1.71512.1850.79228.4075-0.01010.35580.2320.12050.10750.17680.1036-0.2099-0.09740.1197-0.02930.01110.06340.03840.184556.84544.11736.563
22.2111-0.60080.7942.6371-0.41826.2139-0.01430.0017-0.0324-0.1857-0.0226-0.05050.1486-0.03940.03690.1363-0.00960.0040.0202-0.02890.127977.3742.29156.879
34.4685-0.353-1.33991.040.4415.2470.0063-0.07860.4279-0.0950.05570.01250.0288-0.2827-0.0620.1608-0.07420.0160.0347-0.01770.213445.5444.43817.463
43.18470.2881-0.74582.638-0.45735.40020.0044-0.1680.11940.28090.0423-0.07860.1230.1253-0.04670.17040.051-0.010.0413-0.02480.157788.20541.68775.18
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA156 - 1999 - 52
2X-RAY DIFFRACTION1BB200 - 21753 - 70
3X-RAY DIFFRACTION1DC150 - 1602 - 12
4X-RAY DIFFRACTION2AA200 - 21953 - 72
5X-RAY DIFFRACTION2BB158 - 19911 - 52
6X-RAY DIFFRACTION2DD - B150 - 1602 - 12
7X-RAY DIFFRACTION3BB223 - 28276 - 135
8X-RAY DIFFRACTION4AA220 - 28273 - 135
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.232
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.2

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