[English] 日本語

- EMDB-34389: Structure of human phagocyte NADPH oxidase in the resting state -
+
Open data
-
Basic information
Entry | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of human phagocyte NADPH oxidase in the resting state | ||||||||||||
![]() | |||||||||||||
![]() |
| ||||||||||||
![]() | NOX2 / p22 / CYBA / CYBB / TP1170 / NOX / OXIDOREDUCTASE | ||||||||||||
Function / homology | ![]() negative regulation of glomerular filtration by angiotensin / smooth muscle hypertrophy / superoxide-generating NADPH oxidase activity / Oxidoreductases; Acting on NADH or NADPH; With oxygen as acceptor / hypoxia-inducible factor-1alpha signaling pathway / cellular response to L-glutamine / positive regulation of toll-like receptor 2 signaling pathway / positive regulation of defense response to bacterium / mucus secretion / perinuclear endoplasmic reticulum ...negative regulation of glomerular filtration by angiotensin / smooth muscle hypertrophy / superoxide-generating NADPH oxidase activity / Oxidoreductases; Acting on NADH or NADPH; With oxygen as acceptor / hypoxia-inducible factor-1alpha signaling pathway / cellular response to L-glutamine / positive regulation of toll-like receptor 2 signaling pathway / positive regulation of defense response to bacterium / mucus secretion / perinuclear endoplasmic reticulum / superoxide-generating NAD(P)H oxidase activity / Cross-presentation of particulate exogenous antigens (phagosomes) / NADPH oxidase complex / cytochrome complex assembly / respiratory burst / WNT5:FZD7-mediated leishmania damping / response to angiotensin / ROS and RNS production in phagocytes / response to aldosterone / regulation of release of sequestered calcium ion into cytosol / hydrogen peroxide biosynthetic process / superoxide anion generation / positive regulation of mucus secretion / cellular response to cadmium ion / superoxide metabolic process / Detoxification of Reactive Oxygen Species / positive regulation of reactive oxygen species biosynthetic process / cellular response to ethanol / tertiary granule membrane / cellular response to angiotensin / RHO GTPases Activate NADPH Oxidases / monoatomic ion channel complex / RAC2 GTPase cycle / RAC3 GTPase cycle / NADPH binding / specific granule membrane / stress fiber / positive regulation of phagocytosis / positive regulation of endothelial cell proliferation / RAC1 GTPase cycle / response to nutrient / FAD binding / response to interleukin-1 / secretory granule / positive regulation of superoxide anion generation / response to activity / response to nutrient levels / positive regulation of smooth muscle cell proliferation / cellular response to glucose stimulus / establishment of localization in cell / cellular response to gamma radiation / defense response / SH3 domain binding / positive regulation of interleukin-6 production / VEGFA-VEGFR2 Pathway / cellular response to mechanical stimulus / phagocytic vesicle membrane / positive regulation of angiogenesis / positive regulation of tumor necrosis factor production / nuclear envelope / cellular response to tumor necrosis factor / flavin adenine dinucleotide binding / positive regulation of cell growth / monoatomic ion transmembrane transport / response to hypoxia / electron transfer activity / endosome / apical plasma membrane / inflammatory response / response to xenobiotic stimulus / protein heterodimerization activity / innate immune response / focal adhesion / neuronal cell body / heme binding / dendrite / endoplasmic reticulum membrane / Neutrophil degranulation / metal ion binding / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||
![]() | Chen L / Liu R / Song K | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 78.8 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 19 KB 19 KB | Display Display | ![]() |
Images | ![]() | 85.6 KB | ||
Filedesc metadata | ![]() | 6.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 539.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 539.2 KB | Display | |
Data in XML | ![]() | 6.2 KB | Display | |
Data in CIF | ![]() | 7.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8gz3MC C: citing same article ( M: atomic model generated by this map |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05557 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-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 |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
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: ![]() |
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 |
---|---|
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 |