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Yorodumi- EMDB-34390: Consensus map of human phagocyte NADPH oxidase in the resting state -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34390 | ||||||||||||
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Title | Consensus map of human phagocyte NADPH oxidase in the resting state | ||||||||||||
Map data | |||||||||||||
Sample |
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Biological species | Homo sapiens (human) / Mus musculus (house mouse) / Vicugna pacos (alpaca) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||
Authors | Chen L / Liu R | ||||||||||||
Funding support | China, 3 items
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Citation | Journal: Elife / Year: 2022 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34390.map.gz | 79.1 MB | EMDB map data format | |
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Header (meta data) | emd-34390-v30.xml emd-34390.xml | 14.7 KB 14.7 KB | Display Display | EMDB header |
Images | emd_34390.png | 73.8 KB | ||
Masks | emd_34390_msk_1.map | 83.7 MB | Mask map | |
Others | emd_34390_additional_1.map.gz emd_34390_half_map_1.map.gz emd_34390_half_map_2.map.gz | 42.2 MB 77.8 MB 77.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34390 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34390 | HTTPS FTP |
-Validation report
Summary document | emd_34390_validation.pdf.gz | 792 KB | Display | EMDB validaton report |
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Full document | emd_34390_full_validation.pdf.gz | 791.6 KB | Display | |
Data in XML | emd_34390_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | emd_34390_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34390 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34390 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_34390.map.gz / Format: CCP4 / Size: 83.7 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: 1.05557 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_34390_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_34390_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34390_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34390_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : NADPH oxidase2 with Fab and nanobody
Entire | Name: NADPH oxidase2 with Fab and nanobody |
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Components |
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-Supramolecule #1: NADPH oxidase2 with Fab and nanobody
Supramolecule | Name: NADPH oxidase2 with Fab and nanobody / type: complex / ID: 1 / Chimera: Yes / Parent: 0 |
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-Supramolecule #2: NADPH oxidase2
Supramolecule | Name: NADPH oxidase2 / type: complex / ID: 2 / Chimera: Yes / Parent: 1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: Fab
Supramolecule | Name: Fab / type: complex / ID: 3 / Chimera: Yes / Parent: 1 |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Supramolecule #4: anti-Fab nanobody
Supramolecule | Name: anti-Fab nanobody / type: complex / ID: 4 / Chimera: Yes / Parent: 1 |
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Source (natural) | Organism: Vicugna pacos (alpaca) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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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 K2 QUANTUM (4k x 4k) / Average electron dose: 37.6 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: 2.0 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 141189 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |