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Yorodumi- EMDB-37159: Cryo-EM structure of NADPH oxidase 2 in complex with p22phox and EROS -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37159 | |||||||||
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Title | Cryo-EM structure of NADPH oxidase 2 in complex with p22phox and EROS | |||||||||
Map data | ||||||||||
Sample |
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Keywords | NADPH oxidase / IMMUNE SYSTEM | |||||||||
Function / homology | Function and homology information smooth muscle hypertrophy / respiratory burst after phagocytosis / 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 ...smooth muscle hypertrophy / respiratory burst after phagocytosis / 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 / endoplasmic reticulum / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Oryctolagus cuniculus (rabbit) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.56 Å | |||||||||
Authors | Liang SY / Liu AJ / Liu YZ / Ye RD | |||||||||
Funding support | 1 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of NADPH oxidase 2 in complex with p22phox and EROS Authors: Liang SY / Liu AJ / Liu YZ / Ye RD | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37159.map.gz | 229.9 MB | EMDB map data format | |
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Header (meta data) | emd-37159-v30.xml emd-37159.xml | 19.2 KB 19.2 KB | Display Display | EMDB header |
Images | emd_37159.png | 42.3 KB | ||
Filedesc metadata | emd-37159.cif.gz | 6.5 KB | ||
Others | emd_37159_half_map_1.map.gz emd_37159_half_map_2.map.gz | 226.5 MB 226.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37159 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37159 | HTTPS FTP |
-Validation report
Summary document | emd_37159_validation.pdf.gz | 976.1 KB | Display | EMDB validaton report |
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Full document | emd_37159_full_validation.pdf.gz | 975.7 KB | Display | |
Data in XML | emd_37159_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | emd_37159_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37159 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37159 | HTTPS FTP |
-Related structure data
Related structure data | 8keiMC M: atomic model generated by this map C: citing same article (ref.) |
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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_37159.map.gz / Format: CCP4 / Size: 244.1 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: 0.85 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_37159_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_37159_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : NADPH oxidase 2 in complex with Cytochrome b-245 light chain, Cyt...
+Supramolecule #1: NADPH oxidase 2 in complex with Cytochrome b-245 light chain, Cyt...
+Macromolecule #1: Cytochrome b-245 light chain
+Macromolecule #2: Cytochrome b-245 heavy chain
+Macromolecule #3: monoclonal antibody 7G5 heavy chain
+Macromolecule #4: Cytochrome b-245 chaperone 1
+Macromolecule #5: monoclonal antibody 7G5 light chain
+Macromolecule #7: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...
+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
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Material: GOLD |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 52.0 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: 2.5 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 131926 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |