+Open data
-Basic information
Entry | Database: PDB / ID: 8u87 | ||||||
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Title | Structural Basis of Human NOX5 Activation | ||||||
Components | NADPH oxidase 5 | ||||||
Keywords | MEMBRANE PROTEIN / enzyme / oxidase / activation mechanism | ||||||
Function / homology | Function and homology information regulation of fusion of sperm to egg plasma membrane / superoxide-generating NADPH oxidase activity / Oxidoreductases; Acting on NADH or NADPH; With oxygen as acceptor / superoxide-generating NAD(P)H oxidase activity / cytoskeleton-dependent cytokinesis / NADPH oxidase complex / proton channel activity / superoxide anion generation / endothelial cell proliferation / Detoxification of Reactive Oxygen Species ...regulation of fusion of sperm to egg plasma membrane / superoxide-generating NADPH oxidase activity / Oxidoreductases; Acting on NADH or NADPH; With oxygen as acceptor / superoxide-generating NAD(P)H oxidase activity / cytoskeleton-dependent cytokinesis / NADPH oxidase complex / proton channel activity / superoxide anion generation / endothelial cell proliferation / Detoxification of Reactive Oxygen Species / proton transmembrane transport / positive regulation of cytokine production / defense response / positive regulation of reactive oxygen species metabolic process / NADP binding / flavin adenine dinucleotide binding / angiogenesis / calcium ion binding / heme binding / endoplasmic reticulum membrane / apoptotic process / endoplasmic reticulum / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.86 Å | ||||||
Authors | Cui, C. / Jiang, M. / Sun, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Structural Basis of Human NOX5 Activation Authors: Cui, C. / Jiang, M. / Sun, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8u87.cif.gz | 207.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8u87.ent.gz | 161.4 KB | Display | PDB format |
PDBx/mmJSON format | 8u87.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8u87_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8u87_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 8u87_validation.xml.gz | 47.2 KB | Display | |
Data in CIF | 8u87_validation.cif.gz | 66 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u8/8u87 ftp://data.pdbj.org/pub/pdb/validation_reports/u8/8u87 | HTTPS FTP |
-Related structure data
Related structure data | 42016MC 8u7yC 8u85C 8u86C 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 , 1 types, 2 molecules AC
#1: Protein | Mass: 82118.992 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NOX5 / Production host: Homo sapiens (human) References: UniProt: Q96PH1, Oxidoreductases; Acting on NADH or NADPH; With oxygen as acceptor |
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-Non-polymers , 5 types, 10 molecules
#2: Chemical | ChemComp-HEB / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-ZN / | #6: Chemical | ChemComp-D12 / | |
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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: NADPH oxidase 5 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
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: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.20_4459: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 89751 / Symmetry type: POINT | ||||||||||||||||||||||||
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