+Open data
-Basic information
Entry | Database: PDB / ID: 6pat | ||||||
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Title | Active State of Manduca sexta soluble Guanylate Cyclase | ||||||
Components |
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Keywords | SIGNALING PROTEIN / Nitric oxide / cyclase / H-NOX / stimulator | ||||||
Function / homology | Function and homology information guanylate cyclase complex, soluble / guanylate cyclase / guanylate cyclase activity / response to oxygen levels / cGMP-mediated signaling / heme binding / GTP binding Similarity search - Function | ||||||
Biological species | Manduca sexta (tobacco hornworm) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.8 Å | ||||||
Authors | Yokom, A.L. / Horst, B.G. / Marletta, M.A. / Hurley, J.H. | ||||||
Citation | Journal: Elife / Year: 2019 Title: Allosteric activation of the nitric oxide receptor soluble guanylate cyclase mapped by cryo-electron microscopy. Authors: Benjamin G Horst / Adam L Yokom / Daniel J Rosenberg / Kyle L Morris / Michal Hammel / James H Hurley / Michael A Marletta / Abstract: Soluble guanylate cyclase (sGC) is the primary receptor for nitric oxide (NO) in mammalian nitric oxide signaling. We determined structures of full-length sGC in both inactive and active states ...Soluble guanylate cyclase (sGC) is the primary receptor for nitric oxide (NO) in mammalian nitric oxide signaling. We determined structures of full-length sGC in both inactive and active states using cryo-electron microscopy. NO and the sGC-specific stimulator YC-1 induce a 71° rotation of the heme-binding β H-NOX and PAS domains. Repositioning of the β H-NOX domain leads to a straightening of the coiled-coil domains, which, in turn, use the motion to move the catalytic domains into an active conformation. YC-1 binds directly between the β H-NOX domain and the two CC domains. The structural elongation of the particle observed in cryo-EM was corroborated in solution using small angle X-ray scattering (SAXS). These structures delineate the endpoints of the allosteric transition responsible for the major cyclic GMP-dependent physiological effects of NO. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6pat.cif.gz | 144.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pat.ent.gz | 86.5 KB | Display | PDB format |
PDBx/mmJSON format | 6pat.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pat_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6pat_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6pat_validation.xml.gz | 36.6 KB | Display | |
Data in CIF | 6pat_validation.cif.gz | 56.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pa/6pat ftp://data.pdbj.org/pub/pdb/validation_reports/pa/6pat | HTTPS FTP |
-Related structure data
Related structure data | 20283MC 6pasC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 78598.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Manduca sexta (tobacco hornworm) Production host: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths) References: UniProt: O77105 |
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#2: Protein | Mass: 68182.000 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Manduca sexta (tobacco hornworm) Production host: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths) References: UniProt: O77106 |
#3: Chemical | ChemComp-HEM / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Active state of heterodimeric Ms sGC / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Source (natural) | Organism: Manduca sexta (tobacco hornworm) |
Source (recombinant) | Organism: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40469 / Symmetry type: POINT |