+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42015 | |||||||||
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Title | Structural Basis of Human NOX5 Activation | |||||||||
Map data | ||||||||||
Sample |
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Keywords | enzyme / oxidase / activation mechanism / MEMBRANE PROTEIN | |||||||||
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 | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Cui C / Jiang M / Sun J | |||||||||
Funding support | United States, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_42015.map.gz | 117.8 MB | EMDB map data format | |
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Header (meta data) | emd-42015-v30.xml emd-42015.xml | 14.9 KB 14.9 KB | Display Display | EMDB header |
Images | emd_42015.png | 55 KB | ||
Filedesc metadata | emd-42015.cif.gz | 5.7 KB | ||
Others | emd_42015_half_map_1.map.gz emd_42015_half_map_2.map.gz | 115.4 MB 115.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42015 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42015 | HTTPS FTP |
-Validation report
Summary document | emd_42015_validation.pdf.gz | 748.5 KB | Display | EMDB validaton report |
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Full document | emd_42015_full_validation.pdf.gz | 748.1 KB | Display | |
Data in XML | emd_42015_validation.xml.gz | 14 KB | Display | |
Data in CIF | emd_42015_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42015 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42015 | HTTPS FTP |
-Related structure data
Related structure data | 8u86MC 8u7yC 8u85C 8u87C 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_42015.map.gz / Format: CCP4 / Size: 125 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: 0.826 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_42015_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_42015_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : NADPH oxidase 5
Entire | Name: NADPH oxidase 5 |
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Components |
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-Supramolecule #1: NADPH oxidase 5
Supramolecule | Name: NADPH oxidase 5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: NADPH oxidase 5
Macromolecule | Name: NADPH oxidase 5 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO EC number: Oxidoreductases; Acting on NADH or NADPH; With oxygen as acceptor |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 82.118992 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MSAEEDARWL RWVTQQFKTI AGEDGEISLQ EFKAALHVKE SFFAERFFAL FDSDRSGTIT LQELQEALTL LIHGSPMDKL KFLFQVYDI DGSGSIDPDE LRTVLQSCLR ESAISLPDEK LDQLTLALFE SADADGNGAI TFEELRDELQ RFPGVMENLT I SAAHWLTA ...String: MSAEEDARWL RWVTQQFKTI AGEDGEISLQ EFKAALHVKE SFFAERFFAL FDSDRSGTIT LQELQEALTL LIHGSPMDKL KFLFQVYDI DGSGSIDPDE LRTVLQSCLR ESAISLPDEK LDQLTLALFE SADADGNGAI TFEELRDELQ RFPGVMENLT I SAAHWLTA PAPRPRPRRP RQLTRAYWHN HRSQLFCLAT YAGLHVLLFG LAASAHRDLG ASVMVAKGCG QCLNFDCSFI AV LMLRRCL TWLRATWLAQ VLPLDQNIQF HQLMGYVVVG LSLVHTVAHT VNFVLQAQAE ASPFQFWELL LTTRPGIGWV HGS ASPTGV ALLLLLLLMF ICSSSCIRRS GHFEVFYWTH LSYLLVWLLL IFHGPNFWKW LLVPGILFFL EKAIGLAVSR MAAV CIMEV NLLPSKVTHL LIKRPPFFHY RPGDYLYLNI PTIARYEWHP FTISSAPEQK DTIWLHIRSQ GQWTNRLYES FKASD PLGR GSKRLSRSVT MRKSQRSSKG SEILLEKHKF CNIKCYIDGP YGTPTRRIFA SEHAVLIGAG IGITPFASIL QSIMYR HQK RKHTCPSCQH SWIEGVQDNM KLHKVDFIWI NRDQRSFEWF VSLLTKLEMD QAEEAQYGRF LELHMYMTSA LGKNDMK AI GLQMALDLLA NKEKKDSITG LQTRTQPGRP DWSKVFQKVA AEKKGKVQVF FCGSPALAKV LKGHCEKFGF RFFQENF UniProtKB: NADPH oxidase 5 |
-Macromolecule #2: HEME B/C
Macromolecule | Name: HEME B/C / type: ligand / ID: 2 / Number of copies: 4 / Formula: HEB |
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Molecular weight | Theoretical: 618.503 Da |
Chemical component information | ChemComp-HEB: |
-Macromolecule #3: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Macromolecule | Name: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE type: ligand / ID: 3 / Number of copies: 2 / Formula: NDP |
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Molecular weight | Theoretical: 745.421 Da |
Chemical component information | ChemComp-NDP: |
-Macromolecule #4: FLAVIN-ADENINE DINUCLEOTIDE
Macromolecule | Name: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 4 / Number of copies: 2 / Formula: FAD |
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Molecular weight | Theoretical: 785.55 Da |
Chemical component information | ChemComp-FAD: |
-Macromolecule #5: DODECANE
Macromolecule | Name: DODECANE / type: ligand / ID: 5 / Number of copies: 2 / Formula: D12 |
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Molecular weight | Theoretical: 170.335 Da |
Chemical component information | ChemComp-D12: |
-Macromolecule #6: DECANE
Macromolecule | Name: DECANE / type: ligand / ID: 6 / Number of copies: 2 / Formula: D10 |
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Molecular weight | Theoretical: 142.282 Da |
Chemical component information | ChemComp-D10: |
-Macromolecule #7: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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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 K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 201424 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |