+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9886 | |||||||||||||||
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Title | human soluble guanylate cyclase H105C mutant | |||||||||||||||
Map data | composite map after multibody refinement | |||||||||||||||
Sample |
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Function / homology | Function and homology information retrograde trans-synaptic signaling by nitric oxide, modulating synaptic transmission / cytidylate cyclase activity / trans-synaptic signaling by nitric oxide, modulating synaptic transmission / guanylate cyclase complex, soluble / guanylate cyclase / cGMP biosynthetic process / guanylate cyclase activity / response to oxygen levels / presynaptic active zone cytoplasmic component / Nitric oxide stimulates guanylate cyclase ...retrograde trans-synaptic signaling by nitric oxide, modulating synaptic transmission / cytidylate cyclase activity / trans-synaptic signaling by nitric oxide, modulating synaptic transmission / guanylate cyclase complex, soluble / guanylate cyclase / cGMP biosynthetic process / guanylate cyclase activity / response to oxygen levels / presynaptic active zone cytoplasmic component / Nitric oxide stimulates guanylate cyclase / relaxation of vascular associated smooth muscle / adenylate cyclase activity / blood circulation / positive regulation of nitric oxide mediated signal transduction / cGMP-mediated signaling / Smooth Muscle Contraction / cellular response to nitric oxide / nitric oxide mediated signal transduction / GABA-ergic synapse / nitric oxide-cGMP-mediated signaling / Hsp90 protein binding / regulation of blood pressure / signaling receptor activity / glutamatergic synapse / heme binding / GTP binding / protein-containing complex binding / metal ion binding / cytosol Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.8 Å | |||||||||||||||
Authors | Chen L / Kang Y / Liu R / Wu J-X | |||||||||||||||
Funding support | China, 4 items
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Citation | Journal: Nature / Year: 2019 Title: Structural insights into the mechanism of human soluble guanylate cyclase. Authors: Yunlu Kang / Rui Liu / Jing-Xiang Wu / Lei Chen / Abstract: Soluble guanylate cyclase (sGC) is the primary sensor of nitric oxide. It has a central role in nitric oxide signalling and has been implicated in many essential physiological processes and disease ...Soluble guanylate cyclase (sGC) is the primary sensor of nitric oxide. It has a central role in nitric oxide signalling and has been implicated in many essential physiological processes and disease conditions. The binding of nitric oxide boosts the enzymatic activity of sGC. However, the mechanism by which nitric oxide activates the enzyme is unclear. Here we report the cryo-electron microscopy structures of the human sGCα1β1 heterodimer in different functional states. These structures revealed that the transducer module bridges the nitric oxide sensor module and the catalytic module. Binding of nitric oxide to the β1 haem-nitric oxide and oxygen binding (H-NOX) domain triggers the structural rearrangement of the sensor module and a conformational switch of the transducer module from bending to straightening. The resulting movement of the N termini of the catalytic domains drives structural changes within the catalytic module, which in turn boost the enzymatic activity of sGC. | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9886.map.gz | 3.1 MB | EMDB map data format | |
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Header (meta data) | emd-9886-v30.xml emd-9886.xml | 8.8 KB 8.8 KB | Display Display | EMDB header |
Images | emd_9886.png | 39.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9886 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9886 | HTTPS FTP |
-Validation report
Summary document | emd_9886_validation.pdf.gz | 79.7 KB | Display | EMDB validaton report |
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Full document | emd_9886_full_validation.pdf.gz | 78.7 KB | Display | |
Data in XML | emd_9886_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9886 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9886 | HTTPS FTP |
-Related structure data
Related structure data | 9883C 9884C 9885C 6jt0C 6jt1C 6jt2C C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_9886.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | composite map after multibody refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.045 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : human soluble guanylate cyclase
Entire | Name: human soluble guanylate cyclase |
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Components |
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-Supramolecule #1: human soluble guanylate cyclase
Supramolecule | Name: human soluble guanylate cyclase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
-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: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 41710 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |