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Yorodumi- PDB-8kei: Cryo-EM structure of NADPH oxidase 2 in complex with p22phox and EROS -
+Open data
-Basic information
Entry | Database: PDB / ID: 8kei | ||||||
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Title | Cryo-EM structure of NADPH oxidase 2 in complex with p22phox and EROS | ||||||
Components |
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Keywords | IMMUNE SYSTEM / NADPH oxidase | ||||||
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 / respiratory burst after phagocytosis / 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 / cellular response to L-glutamine / positive regulation of toll-like receptor 2 signaling pathway / hypoxia-inducible factor-1alpha signaling pathway / respiratory burst after phagocytosis / 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 / response to nutrient / secretory granule / 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 / endoplasmic reticulum / 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: 3.56 Å | ||||||
Authors | Liang, S.Y. / Liu, A.J. / Liu, Y.Z. / Ye, R.D. | ||||||
Funding support | 1items
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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, S.Y. / Liu, A.J. / Liu, Y.Z. / Ye, R.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8kei.cif.gz | 244.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8kei.ent.gz | 190.2 KB | Display | PDB format |
PDBx/mmJSON format | 8kei.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8kei_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8kei_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8kei_validation.xml.gz | 50.4 KB | Display | |
Data in CIF | 8kei_validation.cif.gz | 71.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ke/8kei ftp://data.pdbj.org/pub/pdb/validation_reports/ke/8kei | HTTPS FTP |
-Related structure data
Related structure data | 37159MC 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
-Cytochrome b-245 ... , 3 types, 3 molecules ABD
#1: Protein | Mass: 14663.218 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 |
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#2: Protein | Mass: 64853.066 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CYBB, NOX2 / Production host: Homo sapiens (human) / References: UniProt: P04839, Oxidoreductases |
#4: Protein | Mass: 18491.500 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CYBC1, C17orf62, EROS / Production host: Homo sapiens (human) / References: UniProt: Q9BQA9 |
-Antibody , 2 types, 2 molecules CE
#3: Antibody | Mass: 23484.305 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human) |
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#5: 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: Homo sapiens (human) |
-Sugars , 2 types, 3 molecules
#6: Polysaccharide | Source method: isolated from a genetically manipulated source #9: Sugar | ChemComp-NAG / | |
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-Non-polymers , 3 types, 4 molecules
#7: Chemical | ChemComp-POV / ( | ||
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#8: Chemical | #10: Chemical | ChemComp-LBN / | |
-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: NADPH oxidase 2 in complex with Cytochrome b-245 light chain, Cytochrome b-245 chaperone 1 and a monoclonal antibody Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT | ||||||||||||
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Source (natural) |
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Source (recombinant) | Organism: Homo sapiens (human) | ||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Specimen support | Grid material: GOLD | ||||||||||||
Vitrification | Cryogen name: ETHANE |
-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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 52 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 131926 / Symmetry type: POINT | ||||||||||||||||||||||||
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