+Open data
-Basic information
Entry | Database: PDB / ID: 7u8g | ||||||
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Title | Cryo-EM structure of the core human NADPH oxidase NOX2 | ||||||
Components |
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Keywords | OXIDOREDUCTASE / heterodimer / complex / NADPH oxidase / enzyme | ||||||
Function / homology | Function and homology information smooth muscle hypertrophy / cellular response to L-glutamine / positive regulation of toll-like receptor 2 signaling pathway / hypoxia-inducible factor-1alpha signaling pathway / superoxide-generating NAD(P)H oxidase activity / positive regulation of defense response to bacterium / mucus secretion / Cross-presentation of particulate exogenous antigens (phagosomes) / perinuclear endoplasmic reticulum / cytochrome complex assembly ...smooth muscle hypertrophy / cellular response to L-glutamine / positive regulation of toll-like receptor 2 signaling pathway / hypoxia-inducible factor-1alpha signaling pathway / superoxide-generating NAD(P)H oxidase activity / positive regulation of defense response to bacterium / mucus secretion / Cross-presentation of particulate exogenous antigens (phagosomes) / perinuclear endoplasmic reticulum / cytochrome complex assembly / NADPH oxidase complex / respiratory burst / WNT5:FZD7-mediated leishmania damping / regulation of release of sequestered calcium ion into cytosol / ROS and RNS production in phagocytes / cellular response to ethanol / Oxidoreductases / superoxide anion generation / response to angiotensin / hydrogen peroxide biosynthetic process / positive regulation of mucus secretion / positive regulation of reactive oxygen species biosynthetic process / monoatomic ion channel complex / response to aldosterone / superoxide metabolic process / Detoxification of Reactive Oxygen Species / tertiary granule membrane / RHO GTPases Activate NADPH Oxidases / RAC2 GTPase cycle / RAC3 GTPase cycle / specific granule membrane / positive regulation of phagocytosis / monoatomic ion transmembrane transport / RAC1 GTPase cycle / cellular response to cadmium ion / bioluminescence / response to nutrient / secretory granule / generation of precursor metabolites and energy / establishment of localization in cell / defense response / VEGFA-VEGFR2 Pathway / SH3 domain binding / phagocytic vesicle membrane / positive regulation of angiogenesis / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / nuclear envelope / flavin adenine dinucleotide binding / oxidoreductase activity / electron transfer activity / endosome / response to xenobiotic stimulus / inflammatory response / protein heterodimerization activity / innate immune response / neuronal cell body / dendrite / heme binding / Neutrophil degranulation / endoplasmic reticulum membrane / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Oryctolagus cuniculus (rabbit) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Noreng, S. / Ota, N. / Sun, Y. / Masureel, M. / Payandeh, J. / Yi, T. / Koerber, J.T. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structure of the core human NADPH oxidase NOX2. Authors: Sigrid Noreng / Naruhisa Ota / Yonglian Sun / Hoangdung Ho / Matthew Johnson / Christopher P Arthur / Kellen Schneider / Isabelle Lehoux / Christopher W Davies / Kyle Mortara / Kit Wong / ...Authors: Sigrid Noreng / Naruhisa Ota / Yonglian Sun / Hoangdung Ho / Matthew Johnson / Christopher P Arthur / Kellen Schneider / Isabelle Lehoux / Christopher W Davies / Kyle Mortara / Kit Wong / Dhaya Seshasayee / Matthieu Masureel / Jian Payandeh / Tangsheng Yi / James T Koerber / Abstract: NOX2 is the prototypical member of the NADPH oxidase NOX superfamily and produces superoxide (O), a key reactive oxygen species (ROS) that is essential in innate and adaptive immunity. Mutations that ...NOX2 is the prototypical member of the NADPH oxidase NOX superfamily and produces superoxide (O), a key reactive oxygen species (ROS) that is essential in innate and adaptive immunity. Mutations that lead to deficiency in NOX2 activity correlate with increased susceptibility to bacterial and fungal infections, resulting in chronic granulomatous disease. The core of NOX2 is formed by a heterodimeric transmembrane complex composed of NOX2 (formerly gp91) and p22, but a detailed description of its structural architecture is lacking. Here, we present the structure of the human NOX2 core complex bound to a selective anti-NOX2 antibody fragment. The core complex reveals an intricate extracellular topology of NOX2, a four-transmembrane fold of the p22 subunit, and an extensive transmembrane interface which provides insights into NOX2 assembly and activation. Functional assays uncover an inhibitory activity of the 7G5 antibody mediated by internalization-dependent and internalization-independent mechanisms. Overall, our results provide insights into the NOX2 core complex architecture, disease-causing mutations, and potential avenues for selective NOX2 pharmacological modulation. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7u8g.cif.gz | 241 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7u8g.ent.gz | 185.2 KB | Display | PDB format |
PDBx/mmJSON format | 7u8g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7u8g_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7u8g_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7u8g_validation.xml.gz | 34.4 KB | Display | |
Data in CIF | 7u8g_validation.cif.gz | 47.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u8/7u8g ftp://data.pdbj.org/pub/pdb/validation_reports/u8/7u8g | HTTPS FTP |
-Related structure data
Related structure data | 26383MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 3 types, 3 molecules ABD
#1: Protein | Mass: 97669.766 Da / Num. of mol.: 1 Fragment: N-terminal 2x streptag followed by EGFP and TEV + thrombin cleavage sites. Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CYBA / Production host: Homo sapiens (human) References: UniProt: A0A6M5E0N3, UniProt: P04839, Oxidoreductases |
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#2: Protein | Mass: 21033.451 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CYBA / Production host: Homo sapiens (human) / References: UniProt: P13498 |
#3: Protein | Mass: 23599.393 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Escherichia phage EcSzw-2 (virus) |
-Antibody / Sugars , 2 types, 4 molecules E
#4: Antibody | Mass: 23521.154 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Escherichia phage EcSzw-2 (virus) |
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#6: Sugar |
-Non-polymers , 2 types, 5 molecules
#5: Chemical | #7: Chemical | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: NOX2 core - Fab 7G5 complex / Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293 |
Buffer solution | pH: 8 / Details: 0.03% DDM, 150 mM NaCl, 20 mM Tris |
Specimen | Conc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: Solarus plasma cleaner (Gatan) / Grid material: GOLD / Grid type: Quantifoil |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: OTHER / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 40.4 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
Software |
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EM software | Name: cryoSPARC / Version: 3.1.0 / Category: image acquisition | ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 70486 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.98 Å2 | ||||||||||||||||||||||||
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