[English] 日本語
![](img/lk-miru.gif)
- EMDB-5865: Single-particle reconstruction of conformation V of ligand-free sGC -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-5865 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Single-particle reconstruction of conformation V of ligand-free sGC | |||||||||
![]() | Single-particle reconstruction of conformation V of ligand-free sGC | |||||||||
![]() |
| |||||||||
![]() | soluble guanylate cyclase / conformational heterogeneity | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 30.0 Å | |||||||||
![]() | Campbell MG / Underbakke ES / Potter CS / Carragher B / Marletta MA | |||||||||
![]() | ![]() Title: Single-particle EM reveals the higher-order domain architecture of soluble guanylate cyclase. Authors: Melody G Campbell / Eric S Underbakke / Clinton S Potter / Bridget Carragher / Michael A Marletta / ![]() Abstract: Soluble guanylate cyclase (sGC) is the primary nitric oxide (NO) receptor in mammals and a central component of the NO-signaling pathway. The NO-signaling pathways mediate diverse physiological ...Soluble guanylate cyclase (sGC) is the primary nitric oxide (NO) receptor in mammals and a central component of the NO-signaling pathway. The NO-signaling pathways mediate diverse physiological processes, including vasodilation, neurotransmission, and myocardial functions. sGC is a heterodimer assembled from two homologous subunits, each comprised of four domains. Although crystal structures of isolated domains have been reported, no structure is available for full-length sGC. We used single-particle electron microscopy to obtain the structure of the complete sGC heterodimer and determine its higher-order domain architecture. Overall, the protein is formed of two rigid modules: the catalytic dimer and the clustered Per/Art/Sim and heme-NO/O2-binding domains, connected by a parallel coiled coil at two hinge points. The quaternary assembly demonstrates a very high degree of flexibility. We captured hundreds of individual conformational snapshots of free sGC, NO-bound sGC, and guanosine-5'-[(α,β)-methylene]triphosphate-bound sGC. The molecular architecture and pronounced flexibility observed provides a significant step forward in understanding the mechanism of NO signaling. | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 15.5 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 14.7 KB 14.7 KB | Display Display | ![]() |
Images | ![]() | 52.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5861C ![]() 5862C ![]() 5863C ![]() 5864C ![]() 5866C ![]() 5867C ![]() 5868C ![]() 5869C ![]() 5870C ![]() 5871C ![]() 5872C ![]() 5873C ![]() 5874C ![]() 5875C ![]() 5876C ![]() 5877C ![]() 5878C ![]() 5879C ![]() 5880C ![]() 5881C ![]() 5882C ![]() 5883C ![]() 5884C C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Single-particle reconstruction of conformation V of ligand-free sGC | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
-Entire : Soluble Guanylate Cyclase, ligand-free
Entire | Name: Soluble Guanylate Cyclase, ligand-free |
---|---|
Components |
|
-Supramolecule #1000: Soluble Guanylate Cyclase, ligand-free
Supramolecule | Name: Soluble Guanylate Cyclase, ligand-free / type: sample / ID: 1000 / Oligomeric state: Heterodimer / Number unique components: 1 |
---|---|
Molecular weight | Experimental: 150 KDa / Theoretical: 150 KDa |
-Macromolecule #1: Soluble Guanylate Cyclase
Macromolecule | Name: Soluble Guanylate Cyclase / type: protein_or_peptide / ID: 1 / Name.synonym: sGC / Number of copies: 1 / Oligomeric state: Heterodimer / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Experimental: 150 KDa / Theoretical: 150 KDa |
Recombinant expression | Organism: ![]() ![]() Recombinant plasmid: pFastBac1/sGCALPHA1 and pFastBac1/sGCBETA1 |
-Experimental details
-Structure determination
Method | negative staining |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.5 / Details: 50 mM TEA, 150 mM NaCl, 5 mM DTT |
---|---|
Staining | Type: NEGATIVE Details: 3 microliters of sample were applied to grid. The specimen was stained twice with 2% uranyl formate, then allowed to air-dry. |
Grid | Details: Glow discharged C-flat grid with 2-micron-diameter holes overlaid by thin 1.5 nm continuous carbon |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-
Electron microscopy
Microscope | FEI TECNAI F20 |
---|---|
Temperature | Average: 298 K |
Date | Jan 26, 2013 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 2204 / Average electron dose: 35 e/Å2 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 80000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC / Tilt angle min: -55 |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
-
Image processing
Details | See publication |
---|---|
CTF correction | Details: Each micrograph |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: OTHER / Software - Name: SPIDER / Number images used: 283 |
Final two d classification | Number classes: 1 |