7D9R

Structure of huamn soluble guanylate cyclase in the riociguat and NO-bound state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Activation mechanism of human soluble guanylate cyclase by stimulators and activators.

Liu, R.Kang, Y.Chen, L.

(2021) Nat Commun 12: 5492-5492

  • DOI: https://doi.org/10.1038/s41467-021-25617-0
  • Primary Citation of Related Structures:  
    7D9R, 7D9S, 7D9T, 7D9U

  • PubMed Abstract: 

    Soluble guanylate cyclase (sGC) is the receptor for nitric oxide (NO) in human. It is an important validated drug target for cardiovascular diseases. sGC can be pharmacologically activated by stimulators and activators. However, the detailed structural mechanisms, through which sGC is recognized and positively modulated by these drugs at high spacial resolution, are poorly understood. Here, we present cryo-electron microscopy structures of human sGC in complex with NO and sGC stimulators, YC-1 and riociguat, and also in complex with the activator cinaciguat. These structures uncover the molecular details of how stimulators interact with residues from both β H-NOX and CC domains, to stabilize sGC in the extended active conformation. In contrast, cinaciguat occupies the haem pocket in the β H-NOX domain and sGC shows both inactive and active conformations. These structures suggest a converged mechanism of sGC activation by pharmacological compounds.


  • Organizational Affiliation

    State Key Laboratory of Membrane Biology, College of Future Technology, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, 100871, Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanylate cyclase soluble subunit alpha-1690Homo sapiensMutation(s): 2 
Gene Names: GUCY1A1GUC1A3GUCSA3GUCY1A3
EC: 4.6.1.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q02108 (Homo sapiens)
Explore Q02108 
Go to UniProtKB:  Q02108
PHAROS:  Q02108
GTEx:  ENSG00000164116 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02108
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanylate cyclase soluble subunit beta-1619Homo sapiensMutation(s): 0 
Gene Names: GUCY1B1GUC1B3GUCSB3GUCY1B3
EC: 4.6.1.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q02153 (Homo sapiens)
Explore Q02153 
Go to UniProtKB:  Q02153
PHAROS:  Q02153
GTEx:  ENSG00000061918 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02153
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
F [auth B]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
G2P
Query on G2P

Download Ideal Coordinates CCD File 
C [auth A]PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
GXTIEXDFEKYVGY-KQYNXXCUSA-N
GZO (Subject of Investigation/LOI)
Query on GZO

Download Ideal Coordinates CCD File 
G [auth B]methyl ~{N}-[4,6-bis(azanyl)-2-[1-[(2-fluorophenyl)methyl]pyrazolo[3,4-b]pyridin-3-yl]pyrimidin-5-yl]-~{N}-methyl-carbamate
C20 H19 F N8 O2
WXXSNCNJFUAIDG-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2016YFA0502004
National Natural Science Foundation of China (NSFC)China31622021
National Natural Science Foundation of China (NSFC)China31821091
National Natural Science Foundation of China (NSFC)China31870833

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-11
    Type: Initial release
  • Version 1.1: 2021-10-13
    Changes: Database references
  • Version 1.2: 2024-05-29
    Changes: Data collection, Refinement description