8HBF | pdb_00008hbf

Structure of human soluble guanylate cyclase in the NO+Rio state at 3.1 angstrom

PDB DOI: https://doi.org/10.2210/pdb8HBF/pdb
EM Map EMD-34627: EMDB EMDataResource

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2022-10-28 Released: 2023-04-19
Deposition Author(s): Chen, L., Liu, R.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 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

NO binds to the distal site of haem in the fully activated soluble guanylate cyclase.

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

(2023) Nitric Oxide 134-135: 17-22

PubMed: 36972843 Search on PubMed
DOI: https://doi.org/10.1016/j.niox.2023.03.002
Primary Citation Related Structures:
8HBE, 8HBF, 8HBH

PubMed Abstract:
Soluble guanylate cyclase (sGC) is the primary receptor for nitric oxide (NO). The binding of NO to the haem of sGC induces a large conformational change in the enzyme and activates its cyclase activity. However, whether NO binds to the proximal site or the distal site of haem in the fully activated state remains under debate. Here, we present cryo-EM maps of sGC in the NO-activated state at high resolutions, allowing the observation of the density of NO. These cryo-EM maps show the binding of NO to the distal site of haem in the NO-activated state.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 149.8 kDa
Atom Count: 8,448
Modeled Residue Count: 1,095
Deposited Residue Count: 1,309
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanylate cyclase soluble subunit alpha-1	A	690	Homo sapiens	Mutation(s): 2 Gene Names: GUCY1A1, GUC1A3, GUCSA3, GUCY1A3 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q02108
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanylate cyclase soluble subunit beta-1	B	619	Homo sapiens	Mutation(s): 0 Gene Names: GUCY1B1, GUC1B3, GUCSB3, GUCY1B3 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q02153
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
G2P Query on G2P Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER C₁₁ H₁₈ N₅ O₁₃ P₃ GXTIEXDFEKYVGY-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GZO (Subject of Investigation/LOI) Query on GZO Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	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		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
NO Query on NO Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	NITRIC OXIDE N O ODUCDPQEXGNKDN-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	3.0

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-04-19

Deposition Author(s):

Chen, L.

Liu, R.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	91957201
National Natural Science Foundation of China (NSFC)	China	31821091
National Natural Science Foundation of China (NSFC)	China	31870833