Structure of human phagocyte NADPH oxidase in the resting state
- State Key Laboratory of Membrane Biology, College of Future Technology, Institute of Molecular Medicine, Peking University, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, China
- National Biomedical Imaging Center, Peking University, China
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, China
- Peking-Tsinghua Center for Life Sciences, Peking University, China
Figures
Figure 1 with 7 supplements
The structure of the human NOX2-p22 complex in the resting state.
(A) Schematic of the NOX2 enzymatic assay. O2- produced by NOX2 are converted into H2O2 by SOD. In the presence of H2O2, horseradish peroxidase (HRP) converts the nonfluorescent Amplex Red into …
Figure 1—figure supplement 1
Protein purification.
(A) Size-exclusion chromatography profile of the NOX2-p22-7D5-TP1170 complex in nanodisc. Fractions between dashes were used for cryo-EM sample preparation. (B) Silver-stained SDS-PAGE gel of …
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Figure 1—figure supplement 1—source data 1
The uncropped and unedited gels for Figure 1—figure supplement 1B.
- https://cdn.elifesciences.org/articles/83743/elife-83743-fig1-figsupp1-data1-v2.zip
Figure 1—figure supplement 2
Image processing.
(A) Representative raw micrograph of NOX2-p22-7D5-TP1170 complex in nanodisc. (B) Two-dimensional (2D) class averages of NOX2-p22-7D5-TP1170 complex. (C) Workflow of the cryo-EM data processing. (D) …
Figure 1—figure supplement 3
Representative local electron density maps contoured at 4.62σ.
(A) Local electron density maps of NOX2. (B) Local electron density maps of p22. (C) Local electron density of POPC. (D) Local electron density maps of haems bound in NOX2. (E) Local electron …
Figure 1—figure supplement 4
Sequence alignment of the NADPH oxidases (NOX) subunit.
The sequences of the Homo sapiens NOX2 (hNOX2, UniProtKB: P04839), H. sapiens NOX1 (hNOX1, UniProtKB: Q9Y5S8), H. sapiens NOX3 (hNOX3, UniProtKB: Q9HBY0), H. sapiens NOX4 (hNOX4, UniProtKB: Q9NPH5), …
Figure 1—figure supplement 5
Sequence alignment of p22 subunit.
The sequences of the Homo sapiens p22 (hp22, UniProtKB: P13498), Mus musculus p22 (mp22, UniProtKB: Q61462), Bos taurus p22 (bp22, UniProtKB: O46521), Danio rerio p22 (drp22, UniProtKB: Q6PH62), and …
Figure 1—figure supplement 6
Structural alignment of NADPH oxidases (NOX) family proteins.
(A) Structural comparison of the transmembrane domain (TMD) of hNOX2 (light blue) and csNOX5 (gray). (B) Structural comparison of the dehydrogenase (DH) domain of hNOX2 (light blue) and csNOX5 …
Figure 1—figure supplement 7
Locations of chronic granulomatous disease (CGD) mutations found in human patients.
(A) Mutations of NOX2 found in CGD patients (annotated in UNIPROT) are mapped onto the structural model of NOX2. Cα positions of mutations are shown as red spheres, NOX2 is shown in a light blue …
Figure 2
The structure of human NOX2.
(A) Structure of NOX2 in cartoon representation, and is colored in the rainbow pattern (N-terminus is blue and C-terminus is red). The phospholipid bilayer is shown as gray layers. (B) A 90°-rotated …
Figure 3
The structure of human p22.
(A) Structure of p22 in cartoon representation, and is colored in the rainbow pattern (N-terminus is blue and C-terminus is red). The phospholipid bilayer is shown as gray layers. (B) The …
Figure 4
The interaction between NOX2 and p22.
(A–C) The open-book view of the interface between NOX2 and p22 in surface representation. NOX2 and p22 are colored in light blue and orange respectively in (A). Residues on NOX2 interacting with p22 …
Figure 5
The movements of the dehydrogenase (DH) domain from the resting NOX2 to the active DUOX1.
(A) Side view of the structural alignment of NOX2 in the resting state (light blue) and DUOX1 in the high-calcium state (yellow) in cartoon representation. Their transmembrane domains (TMD) were …
Figure 6 with 2 supplements
Hypothetic model for NOX2 activation.
(A) Resting state of the phagocyte NADPH oxidase. NOX2, p22, and cytosolic factors are shown as cartoon and colored the same as Figure 1A. (B) Activated state of the phagocyte NADPH oxidase. The …
Figure 6—figure supplement 1
Distinct interaction mode between NOX2-p22 complex and DUOX1-DUOXA1 complex.
(A) Structure of human NOX2 and p22 complex (PDB ID: 8GZ3) in cartoon representation. The colors of each individual domain are the same as in Figure 1I. The approximate boundaries of the …
Figure 6—figure supplement 2
Structural comparison between NOX2-7D5 complex and NOX2-7G5 complex.
(A) Overall structural comparison of human NOX2-7D5 complex between this study (orange and blue, PDB ID: 8GZ3) and NOX2-7G5 complex (pink, PDB ID: 7U8G). (B) Structure of NOX2-7D5 complex in cartoon …
Tables
Table 1
Cryo-EM data collection, refinement, and validation statistics.
| PDB IDEMDB ID | NOX2-p22-7D5-TP11708GZ3EMD-34389EMD-34390*/EMD-34620†/EMD-34622‡/EMD-34621§ |
|---|---|
| Data collection and processing | |
| Magnification | ×165,000 |
| Voltage (kV) | 300 |
| Electron exposure (e-/Å2) | 37.6 |
| Defocus range (μm) | –1.5 to –2.0 |
| Pixel size (Å) | 0.821 |
| Symmetry imposed | C1 |
| Initial particle images (no.) | 541,609 |
| Final particle images (no.) | 84,035 |
| Map resolution (Å) | 2.81*/3.1†/3.1‡/2.75§ |
| FSC threshold | 0.143 |
| Map resolution range (Å) | 250–2.8 |
| Refinement | |
| Initial model used (PDB code) | Alpha Fold 2 |
| Model resolution (Å) | 2.8 |
| FSC threshold | 0.143 |
| Model resolution range (Å) | 250–2.8 |
| Map sharpening B factor (Å2) | –89.6*/–128.9†/–123.3‡/100.1§ |
| Model composition | |
| Non-hydrogen atoms | 8,542 |
| Protein residues | 1,214 |
| Ligands | 9 |
| B factors (Å2) | |
| Protein | 55.46 |
| Ligand | 58.94 |
| R.m.s. deviations | |
| Bond lengths (Å) | 0.011 |
| Bond angles (°) | 1.531 |
| Validation | |
| MolProbity score | 1.60 |
| Clashscore | 5.77 |
| Poor rotamers(%) | 1.74 |
| Ramachandran plot | |
| Favored (%) | 97.49 |
| Allowed (%) | 2.42 |
| Disallowed (%) | 0.08 |
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*
The values of consensus refinement.
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†
The values of focused refinement of mask1 (CH1 + CL + TP1170).
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‡
The values of focused refinement of mask2 (DH domain).
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§
The values of focused refinement of mask3 (core).
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Gene (Homo sapiens) | CYBA | GenBank | AB590173.1 | |
| Gene (Homo sapiens) | CYBB | GenBank | NM_000397.4 | |
| Gene (Homo sapiens) | p47phox | GenBank | NM_000265.7 | |
| Gene (Homo sapiens) | p67phox | GenBank | LT740922.1 | |
| Gene (Homo sapiens) | rac1 | GenBank | NM_006908.5 | |
| Cell line (Spodoptera frugiperda) | Sf9 | Thermo Fisher Scientific | Cat. # 12659017 | RRID:CVCL_0549 |
| Cell line (Homo sapiens) | FreeStyle 293F | Thermo Fisher Scientific | Cat. # R79007 | RRID:CVCL_D603 |
| Transfected construct (human) | NOX2-p22 complex | This paper | Transfected construct (human) | |
| Antibody | Anti-NOX2 7D5 (Mouse monoclonal) | MBL Life Science | Cat. # D162-3 | |
| Recombinant DNA reagent | p22-GFP (plasmid) | This paper | GFP version of p22phox | |
| Recombinant DNA reagent | GFP-TP1170 (plasmid) | This paper; Pleiner et al., 2018 | PMID:29263082 | GFP version of TP1170 |
| Peptide, recombinant protein | SOD | Sigma-Aldrich | Cat. # S2515 | |
| Commercial assay or kit | In-Fusion HD Cloning | Takara Bio | Cat. # 639650 | |
| Chemical compound, drug | Amplex Red | GeneCopoeia | Cat. # C291 | |
| Chemical compound, drug | NADPH | Cayman Chemical | Item No. 9000743 | |
| Software, algorithm | SWISS-MODEL | SWISS-MODEL | RRID:SCR_013032 | |
| Software, algorithm | Chimera | Chimera | RRID:SCR_004097 | |
| Software, algorithm | Coot | Coot | RRID:SCR_014222 | |
| Software, algorithm | Phenix | Phenix | RRID:SCR_014224 |
