|Entry||Database: EMDB / ID: EMD-5863|
|Title||Single-particle reconstruction of conformation III of ligand-free sGC|
|Sample||Soluble Guanylate Cyclase, ligand-freeSoluble guanylyl cyclase|
|Keywords||soluble guanylate cyclase / conformational heterogeneity|
|Biological species||Rattus norvegicus (Norway rat)|
|Method||single particle reconstruction / negative staining / Resolution: 30 Å|
|Authors||Campbell MG / Underbakke ES / Potter CS / Carragher B / Marletta MA|
|Citation||Journal: Proc Natl Acad Sci U S A / Year: 2014|
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.
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_5863.map.gz / Format: CCP4 / Size: 41.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.06 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Soluble Guanylate Cyclase, ligand-free
|Entire||Name: Soluble Guanylate Cyclase, ligand-freeSoluble guanylyl cyclase|
Number of Components: 1 / Oligomeric State: Heterodimer
|Mass||Theoretical: 150 kDa / Experimental: 150 kDa|
-Component #1: protein, Soluble Guanylate Cyclase
|Protein||Name: Soluble Guanylate CyclaseSoluble guanylyl cyclase / a.k.a: sGC / Oligomeric Details: Heterodimer / Recombinant expression: Yes / Number of Copies: 1|
|Mass||Theoretical: 150 kDa / Experimental: 150 kDa|
|Source||Species: Rattus norvegicus (Norway rat)|
|Source (engineered)||Expression System: Spodoptera frugiperda (fall armyworm) / Vector: pFastBac1/sGCALPHA1 and pFastBac1/sGCBETA1 / Cell of expression system: Sf9|
|Specimen||Specimen State: Particle / Method: negative staining|
|Sample solution||Buffer solution: 50 mM TEA, 150 mM NaCl, 5 mM DTT / pH: 7.5|
|Support film||Glow discharged C-flat grid with 2-micron-diameter holes overlaid by thin 1.5 nm continuous carbon|
|Staining||3 microliters of sample were applied to grid. The specimen was stained twice with 2% uranyl formate, then allowed to air-dry.|
|Vitrification||Cryogen Name: NONE|
-Electron microscopy imaging
Model: Tecnai F20 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F20 / Date: Jan 26, 2013|
|Electron gun||Electron Source: FIELD EMISSION GUN / Accelerating Voltage: 200 kV / Electron Dose: 35 e/Å2 / Illumination Mode: FLOOD BEAM|
|Lens||Magnification: 80000 X (nominal) / Cs: 2 mm / Imaging Mode: BRIGHT FIELD / Defocus: 1200 - 2200 nm|
|Specimen Holder||Model: SIDE ENTRY, EUCENTRIC / Tilt Angle: -55 - 0 ° / Temperature: 298|
|Camera||Detector: TVIPS TEMCAM-F416 (4k x 4k)|
|Image acquisition||Number of Digital Images: 2204|
|Processing||Method: single particle reconstruction / Number of Class Averages: 1 / Applied Symmetry: C1 (asymmetric) / Number of Projections: 288 / Details: See publication|
|3D reconstruction||Algorithm: RCT / Software: SPIDER / CTF correction: Each micrograph / Resolution: 30 Å / Resolution Method: FSC 0.5, semi-independent|
-Aug 12, 2020. Covid-19 info
New page: Covid-19 featured information page in EM Navigator.
Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data
-Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
- The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info
+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
+Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
- This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
- Now, EM Navigator and Yorodumi are based on the updated data.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
Result of Omokage search can be filtered by keywords and the database types
Related info.:Omokage search
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
- The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi