8wej

Structure of human phagocyte NADPH oxidase in the activated state

Method: ELECTRON MICROSCOPY D_max: 185.1 Å Quality: REASONABLE

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cytochrome b-245 light chain

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 7 其他Polymer 1 PDB declaration: heptameric（7） Consistent with protein copy count	Chain A； UniProt 1–195	Not recorded	Cytochrome b-245 heavy chain × 1 （P04839） Neutrophil cytosol factor 1 × 1 （P14598） Neutrophil cytosolic factor 2 (65kDa, chronic granulomatous disease, autosomal 2), isoform CRA_a × 1 （A0A024R936） Rac family small GTPase 1 × 1 （A0A8C8XFZ1） 7D5 Fab heavy chain × 1 7D5 Fab light chain × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 MG MAGNESIUM ION × 2 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 FDA DIHYDROFLAVINE-ADENINE DINUCLEOTIDE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.79 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 8WEJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1WLP Solution Structure Of The P22Phox-P47Phox Complex Deposited 2004-06-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 148–167（20 aa） Fragment：Alpha Polypeptide (1-25)	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
7U8G Cryo-EM structure of the core human NADPH oxidase NOX2 Deposited 2022-03-08	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–195（195 aa）	Not recorded	POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 HEM PROTOPORPHYRIN IX CONTAINING FE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；0.03% DDM, 150 mM NaCl, 20 mM Tris cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7YXW Structure of the p22phox A200G mutant in complex with p47phox peptide Deposited 2022-02-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 151–168（18 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1 M HEPES pH 7.5, 1.2 M sodium citrate tribasic dihydrate, 1:1 protein:precipitant ratio	Resolution 2.50 Å R-free 0.269
8GZ3 Structure of human phagocyte NADPH oxidase in the resting state Deposited 2022-09-24	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–195（195 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 LBN 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8KEI Cryo-EM structure of NADPH oxidase 2 in complex with p22phox and EROS Deposited 2023-08-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 3–135（133 aa）	Not recorded	POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 LBN 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.56 Å
8X2L Structure of human phagocyte NADPH oxidase in the resting state in the presence of 2 mM NADPH Deposited 2023-11-09	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–195（195 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.99 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CY24A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–195； UniProt 1–195

Cytochrome b-245 heavy chain

Homo sapiens

UniProt P04839

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 7 其他Polymer 1 PDB declaration: heptameric（7） Consistent with protein copy count	Chain B； UniProt 1–570	Not recorded	Cytochrome b-245 light chain × 1 （P13498） Neutrophil cytosol factor 1 × 1 （P14598） Neutrophil cytosolic factor 2 (65kDa, chronic granulomatous disease, autosomal 2), isoform CRA_a × 1 （A0A024R936） Rac family small GTPase 1 × 1 （A0A8C8XFZ1） 7D5 Fab heavy chain × 1 7D5 Fab light chain × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 MG MAGNESIUM ION × 2 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 FDA DIHYDROFLAVINE-ADENINE DINUCLEOTIDE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.79 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8WEJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3A1F The crystal structure of NADPH binding domain of gp91(phox) Deposited 2009-04-01	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 385–570（186 aa） Fragment：UNP residues 385-570	Not recorded	NI NICKEL (II) ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；12% PEG 3350, 0.1M sodium acetate pH 5.6, 0.4M NiCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.00 Å R-free 0.277
7U8G Cryo-EM structure of the core human NADPH oxidase NOX2 Deposited 2022-03-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 2–570（569 aa） Fragment：N-terminal 2x streptag followed by EGFP and TEV + thrombin cleavage sites.	Not recorded	POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 HEM PROTOPORPHYRIN IX CONTAINING FE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；0.03% DDM, 150 mM NaCl, 20 mM Tris cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8GZ3 Structure of human phagocyte NADPH oxidase in the resting state Deposited 2022-09-24	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–570（570 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 LBN 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8KEI Cryo-EM structure of NADPH oxidase 2 in complex with p22phox and EROS Deposited 2023-08-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 6–570（565 aa）	Not recorded	POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 LBN 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.56 Å
8X2L Structure of human phagocyte NADPH oxidase in the resting state in the presence of 2 mM NADPH Deposited 2023-11-09	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–570（570 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.99 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CY24B_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–570； UniProt 1–570

Neutrophil cytosol factor 1

Homo sapiens

UniProt P14598

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 7 其他Polymer 1 PDB declaration: heptameric（7） Consistent with protein copy count	Chain C； UniProt 1–286	Not recorded	Cytochrome b-245 light chain × 1 （P13498） Cytochrome b-245 heavy chain × 1 （P04839） Neutrophil cytosolic factor 2 (65kDa, chronic granulomatous disease, autosomal 2), isoform CRA_a × 1 （A0A024R936） Rac family small GTPase 1 × 1 （A0A8C8XFZ1） 7D5 Fab heavy chain × 1 7D5 Fab light chain × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 MG MAGNESIUM ION × 2 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 FDA DIHYDROFLAVINE-ADENINE DINUCLEOTIDE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.79 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8WEJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1GD5 SOLUTION STRUCTURE OF THE PX DOMAIN FROM HUMAN P47PHOX NADPH OXIDASE Deposited 2000-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–128（128 aa） Fragment：PX DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；293 K；Ionic strength (raw mmCIF value) 0；Pressure 1 NMR sample composition 0.6mM PX domain U-15N,13C; 5mM Na-MES buffer; 95% H2O, 5% D2O \| 95% H2O/5% D2O	Resolution not provided
1K4U Solution structure of the C-terminal SH3 domain of p67phox complexed with the C-terminal tail region of p47phox Deposited 2001-10-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 359–390（32 aa） Fragment：TAIL PEPTIDE (RESIDUES 359-390)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.1；298 K；Ionic strength (raw mmCIF value) 100mM KCl；Pressure 1 NMR sample composition 0.7mM p67SH3(C) U-15N,13C; 0.77mM p47 tail peptide; 5mM MOPSO buffer; 30 mM d10-DTT; 100mM KCl \| 90% H2O, 10% D2O; 100% D2O NMR sample composition 0.5mM p47 tail peptide U-15N,13C; 0.55mM p67SH3(C); 5mM MOPSO buffer; 30mM d10-DTT; 100mM KCl \| 90% H2O, 10% D2O; 100% D2O	Resolution not provided
1KQ6 p47phox PX domain Deposited 2002-01-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–141（141 aa） Fragment：PX domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 3 GOL GLYCEROL × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；291 K；PEG 550 DME, glycerol, ammonium sulfate, natrium citrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.18 Å R-free 0.185
1NG2 Structure of autoinhibited p47phox Deposited 2002-12-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 156–340（185 aa） Fragment：residues 156-340	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；PEG 3000, sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.70 Å R-free 0.233
1NG2 Structure of autoinhibited p47phox Deposited 2002-12-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 156–340（185 aa） Fragment：residues 156-340	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；PEG 3000, sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.70 Å R-free 0.233
1O7K human p47 PX domain complex with sulphates Deposited 2002-11-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–123（123 aa） Fragment：PX DOMAIN, RESIDUES 1-123 Chain B 1–123（123 aa） Fragment：PX DOMAIN, RESIDUES 1-123 Chain C 1–123（123 aa） Fragment：PX DOMAIN, RESIDUES 1-123	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；1 M AMMONIUM SULPHATE, 0.1M TRIS PH 8.5, 12% GLYCEROL	Resolution 2.00 Å R-free 0.254
1OV3 Structure of the p22phox-p47phox complex Deposited 2003-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–285（130 aa） Fragment：Residues 156-285 Chain B 156–285（130 aa） Fragment：Residues 156-285	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；1 M Na-Citrate, 0.1 M Na-cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.80 Å R-free 0.275
1OV3 Structure of the p22phox-p47phox complex Deposited 2003-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 156–285（130 aa） Fragment：Residues 156-285 Chain B 156–285（130 aa） Fragment：Residues 156-285	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；1 M Na-Citrate, 0.1 M Na-cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.80 Å R-free 0.275
1UEC Crystal structure of autoinhibited form of tandem SH3 domain of p47phox Deposited 2003-05-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 151–340（190 aa） Fragment：autoinhibited tandem SH3 domain, redidues 151-340	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.4；293 K；16% PEG 6000, 0.1M soduim citrate, 50mM sodium fluoride, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.82 Å R-free 0.236
1UEC Crystal structure of autoinhibited form of tandem SH3 domain of p47phox Deposited 2003-05-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 151–340（190 aa） Fragment：autoinhibited tandem SH3 domain, redidues 151-340	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.4；293 K；16% PEG 6000, 0.1M soduim citrate, 50mM sodium fluoride, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.82 Å R-free 0.236
1W70 SH3 domain of p40phox complexed with C-terminal polyProline region of p47phox Deposited 2004-08-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 360–372（13 aa） Fragment：POLYPROLINE MOTIF, RESIDUES 360-372	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；VAPOR DIFFUSION AT 20 DEGRE C AT 14MG/ML OF P40PHOX SH3 WITH A1/5 RATIO WITH POLYPROLINE PEPTIDE, 20 MM HEPES PH 7.5, 150 MM NACL MIXED WITH 100 MM NA-CITRATE/CITRIC ACID PH5, 2.4 M SA	Resolution 1.46 Å R-free 0.207
1W70 SH3 domain of p40phox complexed with C-terminal polyProline region of p47phox Deposited 2004-08-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 360–372（13 aa） Fragment：POLYPROLINE MOTIF, RESIDUES 360-372	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 3 TFA trifluoroacetic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；VAPOR DIFFUSION AT 20 DEGRE C AT 14MG/ML OF P40PHOX SH3 WITH A1/5 RATIO WITH POLYPROLINE PEPTIDE, 20 MM HEPES PH 7.5, 150 MM NACL MIXED WITH 100 MM NA-CITRATE/CITRIC ACID PH5, 2.4 M SA	Resolution 1.46 Å R-free 0.207
1WLP Solution Structure Of The P22Phox-P47Phox Complex Deposited 2004-06-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 151–286（136 aa） Fragment：Tandem SH3 domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
7YXW Structure of the p22phox A200G mutant in complex with p47phox peptide Deposited 2022-02-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 156–285（130 aa）	Mutation：A200G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1 M HEPES pH 7.5, 1.2 M sodium citrate tribasic dihydrate, 1:1 protein:precipitant ratio	Resolution 2.50 Å R-free 0.269

10 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NCF1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–286； UniProt 1–286

Neutrophil cytosolic factor 2 (65kDa, chronic granulomatous disease, autosomal 2), isoform CRA_a

Homo sapiens

UniProt A0A024R936

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 7 其他Polymer 1 PDB declaration: heptameric（7） Consistent with protein copy count	Chain D； UniProt 1–306	Not recorded	Cytochrome b-245 light chain × 1 （P13498） Cytochrome b-245 heavy chain × 1 （P04839） Neutrophil cytosol factor 1 × 1 （P14598） Rac family small GTPase 1 × 1 （A0A8C8XFZ1） 7D5 Fab heavy chain × 1 7D5 Fab light chain × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 MG MAGNESIUM ION × 2 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 FDA DIHYDROFLAVINE-ADENINE DINUCLEOTIDE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.79 Å

Other States of the Same Protein in the Database

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	A0A024R936_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–306； UniProt 1–306

Rac family small GTPase 1

Homo sapiens

UniProt A0A8C8XFZ1

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 7 其他Polymer 1 PDB declaration: heptameric（7） Consistent with protein copy count	Chain E； UniProt 1–192	Not recorded	Cytochrome b-245 light chain × 1 （P13498） Cytochrome b-245 heavy chain × 1 （P04839） Neutrophil cytosol factor 1 × 1 （P14598） Neutrophil cytosolic factor 2 (65kDa, chronic granulomatous disease, autosomal 2), isoform CRA_a × 1 （A0A024R936） 7D5 Fab heavy chain × 1 7D5 Fab light chain × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 MG MAGNESIUM ION × 2 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 FDA DIHYDROFLAVINE-ADENINE DINUCLEOTIDE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.79 Å

Other States of the Same Protein in the Database

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	A0A8C8XFZ1_PANLE
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–192； UniProt 1–192

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8wej
Deposition date deposition_date	2023-09-18
Structure title title	Structure of human phagocyte NADPH oxidase in the activated state
Keywords keywords	NOX2, p22, CYBA, CYBB, TP1170, NOX, p67, Rac, p47, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	48.95 Å
Radius of gyration Rg (electron density) rg_electron	50.08 Å
Forward intensity I(0) i0	313699000.00
Molecular weight molecular_weight	151170.0 kDa
Excluded volume excluded_volume	191210 Å³
Envelope volume envelope_volume	248330 Å³
Hydration-shell volume shell_volume	47549 Å³
Envelope diameter envelope_diameter	191.1 Å
Shell Rg shell_rg	44.73 Å
Envelope Rg envelope_rg	50.17 Å
Shape Rg shape_rg	50.07 Å
Total Rg total_rg	49.87 Å
Total atoms total_atoms	10658
Residues n_residues	1336
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	185.1 Å
Rg (real space) rg_real	50.14 Å
Rg uncertainty (real space) rg_real_error	3.09 Å
I(0) (real space) i0_real	3.1370e+08
I(0) uncertainty (real space) i0_real_error	7.0270e+06
Rg (reciprocal space) rg_reciprocal	48.96 Å
I(0) (reciprocal space) i0_reciprocal	313200000.0000
Solution quality estimate total_estimate	0.7067
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	34.7 Å
Skewness Skewness skewness	0.681
Kurtosis Kurtosis kurtosis	-0.151
Angular range angular_range	— – 0.1600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15090000.0000
Real-space data points n_real_points	33
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.452; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.280; Smooth: 0.547

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (15)

Entity 1 Entity 1 polymer

Description description	Cytochrome b-245 light chain
Molecular weight formula_weight	21005.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	10659

MGQIEWAMWANEQALASGLILITGGIVATAGRFTQWYFGAYSIVAGVFVCLLEYPRGKRKKGSTMERWGQKYMTAVVKLFGPFTRNYYVRAVLHLLLSVPAGFLLATILGTACLAIASGIYLLAAVRGEQWTPIEPKPRERPQIGGTIKQPPSNPPPRPPAEARKKPSEEEAAAAAGGPPGGPQVNPIPVTDEVV

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Cytochrome b-245 heavy chain
Molecular weight formula_weight	65412.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MGNWAVNEGLSIFVILVWLGLNVFLFVWYYRVYDIPPKFFYTRKLLGSALALARAPAACLNFNCMLILLPVCRNLLSFLRGSSACCSTRVRRQLDRNLTFHKMVAWMIALHSAIHTIAHLFNVEWCVNARVNNSDPYSVALSELGDRQNESYLNFARKRIKNPEGGLYLAVTLLAGITGVVITLCLILIITSSTKTIRRSYFEVFWYTHHLFVIFFIGLAIHGAERIVRGQTAESLAVHNITVCEQKISEWGKIKECPIPQFAGNPPMTWKWIVGPMFLYLCERLVRFWRSQQKVVITKVVTHPFKTIELQMKKKGFKMEVGQYIFVKCPKVSKLEWHPFTLTSAPEEDFFSIHIRIVGDWTEGLFNACGCDKQEFQDAWKLPKIAVDGPFGTASEDVFSYEVVMLVGAGIGVTPFASILKSVWYKYCNNATNLKLKKIYFYWLCRDTHAFEWFADLLQLLESQMQERNNAGFLSYNIYLTGWDESQANHFAVHHDEEKDVITGLKQKTLYGRPNWDNEFKTIASQHPNTRIGVFLCGPEALAETLSKQSISNSESGPRGVHFIFNKENF

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Neutrophil cytosol factor 1
Molecular weight formula_weight	32813.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MGDTFIRHIALLGFEKRFVPSQHYVYMFLVKWQDLSEKVVYRRFTEIYEFHKTLKEMFPIEAGAINPENRIIPHLPAPKWFDGQRAAENRQGTLTEYCSTLMSLPTKISRCPHLLDFFKVRPDDLKLPTDNQTKKPETYLMPKDGKSTATDITGPIILQTYRAIANYEKTSGSEMALSTGDVVEVVEKSESGWWFCQMKAKRGWIPASFLEPLDSPDETEDPEPNYAGEPYVAIKAYTAVEGDEVSLLEGEAVEVIHKLLDGWWVIRKDDVTGYFPSMYLQKSGQD

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	Neutrophil cytosolic factor 2 (65kDa, chronic granulomatous disease, autosomal 2), isoform CRA_a
Molecular weight formula_weight	34978.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MSLVEAISLWNEGVLAADKKDWKGALDAFSAVQDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKHLAVAYFQRGMLYYQTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKSEPRHSKIDKAMECVWKQKLYEPVVIPVGRLFRPNERQVAQLAKKDYLGKATVVASVVDQDSFSGFAPLQPQAAEPPPRPKTPEIFRALEGEAHRVLFGFVPETKEELQVMPGNIVFVLKKGNDNWATVMFNGQKGLVPCNYLEPVELRIHPQQQ

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 5 Entity 5 polymer

Description description	Rac family small GTPase 1
Molecular weight formula_weight	21463.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGLEDYDRLRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSALTQRGLKTVFDEAIRAVLCPPPVKKRKRKCLLL

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 6 Entity 6 polymer

Description description	7D5 Fab heavy chain
Molecular weight formula_weight	27603.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MKKNIAFLLASMFVFSIATNAYADVQLQESGPGLVKPSQSLSLTCSVTGYSLTSGSFWSWIRQFPGNKLEWMGYITYDGTSHFNPSLKSRFSITRDTSKNQFFLKLNSVTTEDTATYYCTRDPYRYDAMDFWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDLEHHHHHH

来源 Source

来源生物 organism	Mus musculus
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 7 Entity 7 polymer

Description description	7D5 Fab light chain
Molecular weight formula_weight	26238.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MKKNIAFLLASMFVFSIATNAYADIQLTQTTSSLSASLGDRVTISCRASQDISNYLNWYQQKPDGTVKLLIYYTSKLHSGVPSRFTASGSGRDYSLAISNLEQEDIATYFCQQVFSLPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE

来源 Source

来源生物 organism	Mus musculus
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 8 Entity 8 branched

Description description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	586.5 kDa
Source method src_method	man
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 11 Entity 11 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 12 Entity 12 non-polymer

Description description	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Molecular weight formula_weight	745.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 13 Entity 13 non-polymer

Description description	DIHYDROFLAVINE-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	787.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 14 Entity 14 non-polymer

Description description	GUANOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 15 Entity 15 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.79 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	209359

fit	/app/data/saxs_computation/we/8wej/8wej.fit
pddf	/app/data/pr_computation/we/8wej/8wej.pr.out
profile	/app/data/saxs_computation/we/8wej/8wej.dat

Structure of human phagocyte NADPH oxidase in the activated state

1. Protein Identity and Related Structures Protein Identity & Related Structures

Cytochrome b-245 light chain

State in the Current Structure

Other States of the Same Protein in the Database

Cytochrome b-245 heavy chain

State in the Current Structure

Other States of the Same Protein in the Database

Neutrophil cytosol factor 1

State in the Current Structure

Other States of the Same Protein in the Database

Neutrophil cytosolic factor 2 (65kDa, chronic granulomatous disease, autosomal 2), isoform CRA_a

State in the Current Structure

Other States of the Same Protein in the Database

Rac family small GTPase 1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (15)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 polymer

Polymer Polymer

来源 Source

Entity 6 Entity 6 polymer

Polymer Polymer

来源 Source

Entity 7 Entity 7 polymer

Polymer Polymer

来源 Source

Entity 8 Entity 8 branched

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 non-polymer

Entity 13 Entity 13 non-polymer

Entity 14 Entity 14 non-polymer

Entity 15 Entity 15 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)