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- PDB-9bcv: Cyclase domain of GC-A bound to ANP -

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Basic information

Entry
Database: PDB / ID: 9bcv
TitleCyclase domain of GC-A bound to ANP
Components
  • Atrial natriuretic peptide receptor 1
  • Fab fragment
KeywordsLYASE / Single pass transmembrane protein / guanylyl cyclase / atrial natriuretic peptide receptor / hypertension / membrane protein
Function / homology
Function and homology information


ANPR-A receptor complex / natriuretic peptide receptor activity / positive regulation of cGMP-mediated signaling / receptor guanylyl cyclase signaling pathway / body fluid secretion / peptide receptor activity / positive regulation of renal sodium excretion / guanylate cyclase / cGMP biosynthetic process / guanylate cyclase activity ...ANPR-A receptor complex / natriuretic peptide receptor activity / positive regulation of cGMP-mediated signaling / receptor guanylyl cyclase signaling pathway / body fluid secretion / peptide receptor activity / positive regulation of renal sodium excretion / guanylate cyclase / cGMP biosynthetic process / guanylate cyclase activity / Physiological factors / hormone binding / regulation of vascular permeability / positive regulation of urine volume / G protein-coupled peptide receptor activity / adenylate cyclase activity / cGMP-mediated signaling / dopamine metabolic process / peptide hormone binding / negative regulation of angiogenesis / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / negative regulation of cell growth / regulation of blood pressure / receptor complex / cell surface receptor signaling pathway / protein kinase activity / GTP binding / ATP binding / plasma membrane
Similarity search - Function
Adenylyl cyclase class-4/guanylyl cyclase / Natriuretic peptides receptors signature. / : / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylate and Guanylate cyclase catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Guanylate cyclase domain profile. / Nucleotide cyclase ...Adenylyl cyclase class-4/guanylyl cyclase / Natriuretic peptides receptors signature. / : / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylate and Guanylate cyclase catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Guanylate cyclase domain profile. / Nucleotide cyclase / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Atrial natriuretic peptide receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLiu, S. / Huang, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM138676 United States
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Architecture and activation of single-pass transmembrane receptor guanylyl cyclase.
Authors: Shian Liu / Alexander M Payne / Jinan Wang / Lan Zhu / Navid Paknejad / Edward T Eng / Wei Liu / Yinglong Miao / Richard K Hite / Xin-Yun Huang /
Abstract: The heart, in addition to its primary role in blood circulation, functions as an endocrine organ by producing cardiac hormone natriuretic peptides. These hormones regulate blood pressure through the ...The heart, in addition to its primary role in blood circulation, functions as an endocrine organ by producing cardiac hormone natriuretic peptides. These hormones regulate blood pressure through the single-pass transmembrane receptor guanylyl cyclase A (GC-A), also known as natriuretic peptide receptor 1. The binding of the peptide hormones to the extracellular domain of the receptor activates the intracellular guanylyl cyclase domain of the receptor to produce the second messenger cyclic guanosine monophosphate. Despite their importance, the detailed architecture and domain interactions within full-length GC-A remain elusive. Here we present cryo-electron microscopy structures, functional analyses and molecular dynamics simulations of full-length human GC-A, in both the absence and the presence of atrial natriuretic peptide. The data reveal the architecture of full-length GC-A, highlighting the spatial arrangement of its various functional domains. This insight is crucial for understanding how different parts of the receptor interact and coordinate during activation. The study elucidates the molecular basis of how extracellular signals are transduced across the membrane to activate the intracellular guanylyl cyclase domain.
History
DepositionApr 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Atrial natriuretic peptide receptor 1
B: Atrial natriuretic peptide receptor 1
G: Fab fragment
H: Fab fragment
J: Fab fragment
I: Fab fragment
C: Fab fragment
D: Fab fragment
E: Fab fragment
F: Fab fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,05714
Polymers312,96610
Non-polymers1,0914
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Atrial natriuretic peptide receptor 1 / Atrial natriuretic peptide receptor type A / ANP-A / ANPR-A / NPR-A / Guanylate cyclase A / GC-A


Mass: 115560.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NPR1, ANPRA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P16066, guanylate cyclase
#2: Antibody
Fab fragment


Mass: 10230.603 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-G2P / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GMP-CPP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Atrial natriuretic peptide receptor 1 dimer / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 112661 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037779
ELECTRON MICROSCOPYf_angle_d0.53410757
ELECTRON MICROSCOPYf_dihedral_angle_d4.691365
ELECTRON MICROSCOPYf_chiral_restr0.041425
ELECTRON MICROSCOPYf_plane_restr0.0031457

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