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Yorodumi- EMDB-34389: Structure of human phagocyte NADPH oxidase in the resting state -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34389 | ||||||||||||
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Title | Structure of human phagocyte NADPH oxidase in the resting state | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | NOX2 / p22 / CYBA / CYBB / TP1170 / NOX / OXIDOREDUCTASE | ||||||||||||
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 / ROS and RNS production in phagocytes / regulation of release of sequestered calcium ion into cytosol / Oxidoreductases / cellular response to ethanol / superoxide anion generation / response to angiotensin / hydrogen peroxide biosynthetic process / positive regulation of mucus secretion / monoatomic ion channel complex / positive regulation of reactive oxygen species biosynthetic process / 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 / cellular response to cadmium ion / RAC1 GTPase cycle / response to nutrient / secretory granule / establishment of localization in cell / defense response / SH3 domain binding / VEGFA-VEGFR2 Pathway / positive regulation of interleukin-6 production / positive regulation of angiogenesis / phagocytic vesicle membrane / positive regulation of tumor necrosis factor production / monoatomic ion transmembrane transport / nuclear envelope / flavin adenine dinucleotide binding / electron transfer activity / oxidoreductase activity / endosome / inflammatory response / response to xenobiotic stimulus / 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) / Mus musculus (house mouse) / Vicugna pacos (alpaca) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||
Authors | Chen L / Liu R / Song K | ||||||||||||
Funding support | China, 3 items
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Citation | Journal: Elife / Year: 2022 Title: Structure of human phagocyte NADPH oxidase in the resting state. Authors: Rui Liu / Kangcheng Song / Jing-Xiang Wu / Xiao-Peng Geng / Liming Zheng / Xiaoyin Gao / Hailin Peng / Lei Chen / Abstract: Phagocyte oxidase plays an essential role in the first line of host defense against pathogens. It oxidizes intracellular NADPH to reduce extracellular oxygen to produce superoxide anions that ...Phagocyte oxidase plays an essential role in the first line of host defense against pathogens. It oxidizes intracellular NADPH to reduce extracellular oxygen to produce superoxide anions that participate in pathogen killing. The resting phagocyte oxidase is a heterodimeric complex formed by two transmembrane proteins NOX2 and p22. Despite the physiological importance of this complex, its structure remains elusive. Here, we reported the cryo-EM structure of the functional human NOX2-p22 complex in nanodisc in the resting state. NOX2 shows a canonical 6-TM architecture of NOX and p22 has four transmembrane helices. M3, M4, and M5 of NOX2, and M1 and M4 helices of p22 are involved in the heterodimer formation. Dehydrogenase (DH) domain of NOX2 in the resting state is not optimally docked onto the transmembrane domain, leading to inefficient electron transfer and NADPH binding. Structural analysis suggests that the cytosolic factors might activate the NOX2-p22 complex by stabilizing the DH in a productive docked conformation. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34389.map.gz | 78.8 MB | EMDB map data format | |
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Header (meta data) | emd-34389-v30.xml emd-34389.xml | 19 KB 19 KB | Display Display | EMDB header |
Images | emd_34389.png | 85.6 KB | ||
Filedesc metadata | emd-34389.cif.gz | 6.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34389 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34389 | HTTPS FTP |
-Validation report
Summary document | emd_34389_validation.pdf.gz | 539.6 KB | Display | EMDB validaton report |
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Full document | emd_34389_full_validation.pdf.gz | 539.2 KB | Display | |
Data in XML | emd_34389_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | emd_34389_validation.cif.gz | 7.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34389 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34389 | HTTPS FTP |
-Related structure data
Related structure data | 8gz3MC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_34389.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05557 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : NADPH oxidase2
+Supramolecule #1: NADPH oxidase2
+Macromolecule #1: Cytochrome b-245 light chain
+Macromolecule #2: Cytochrome b-245 heavy chain
+Macromolecule #3: 7D5 Fab light chain
+Macromolecule #4: 7D5 Fab heavy chain
+Macromolecule #5: Green Fluorescent Protein, Anti-Fab (kappa) nanobody[TP1170] chimera
+Macromolecule #7: FLAVIN-ADENINE DINUCLEOTIDE
+Macromolecule #8: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose
+Macromolecule #10: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
+Macromolecule #11: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 37.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 84035 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |