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- PDB-9bcq: Extracellular domain of GC-A bound to ANP -

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Basic information

Entry
Database: PDB / ID: 9bcq
TitleExtracellular domain of GC-A bound to ANP
Components(Atrial natriuretic ...) x 2
KeywordsLYASE / Single pass transmembrane protein / guanylyl cyclase / atrial natriuretic peptide receptor / hypertension / membrane protein
Function / homology
Function and homology information


positive regulation of delayed rectifier potassium channel activity / ANPR-A receptor complex / natriuretic peptide receptor activity / positive regulation of cGMP-mediated signaling / neuropeptide receptor binding / receptor guanylyl cyclase signaling pathway / body fluid secretion / regulation of high voltage-gated calcium channel activity / positive regulation of potassium ion export across plasma membrane / peptide receptor activity ...positive regulation of delayed rectifier potassium channel activity / ANPR-A receptor complex / natriuretic peptide receptor activity / positive regulation of cGMP-mediated signaling / neuropeptide receptor binding / receptor guanylyl cyclase signaling pathway / body fluid secretion / regulation of high voltage-gated calcium channel activity / positive regulation of potassium ion export across plasma membrane / peptide receptor activity / positive regulation of renal sodium excretion / guanylate cyclase / regulation of atrial cardiac muscle cell membrane repolarization / cGMP biosynthetic process / guanylate cyclase activity / Physiological factors / cardiac conduction system development / hormone binding / YAP1- and WWTR1 (TAZ)-stimulated gene expression / regulation of vascular permeability / negative regulation of JUN kinase activity / sodium ion export across plasma membrane / positive regulation of urine volume / neuropeptide hormone activity / cardiac muscle hypertrophy in response to stress / G protein-coupled peptide receptor activity / hormone receptor binding / negative regulation of systemic arterial blood pressure / aortic valve morphogenesis / adenylate cyclase activity / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / positive regulation of heart rate / cGMP-mediated signaling / dopamine metabolic process / peptide hormone binding / neuropeptide signaling pathway / positive regulation of cardiac muscle contraction / response to muscle stretch / negative regulation of angiogenesis / blood vessel diameter maintenance / cell projection / female pregnancy / negative regulation of smooth muscle cell proliferation / negative regulation of cell growth / hormone activity / regulation of blood pressure / vasodilation / protein folding / perikaryon / collagen-containing extracellular matrix / receptor complex / cell surface receptor signaling pathway / protein kinase activity / Amyloid fiber formation / signaling receptor binding / GTP binding / protein-containing complex / extracellular space / extracellular region / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Natriuretic peptide, atrial type / : / Natriuretic peptide, conserved site / Atrial natriuretic peptide / Natriuretic peptides signature. / Natriuretic peptide / Natriuretic peptide / Adenylyl cyclase class-4/guanylyl cyclase / Natriuretic peptides receptors signature. / : ...Natriuretic peptide, atrial type / : / Natriuretic peptide, conserved site / Atrial natriuretic peptide / Natriuretic peptides signature. / Natriuretic peptide / Natriuretic peptide / 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
Natriuretic peptides A / Atrial natriuretic peptide receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 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
C: Atrial natriuretic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,78110
Polymers236,6293
Non-polymers2,1527
Water00
1


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

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Components

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Atrial natriuretic ... , 2 types, 3 molecules ABC

#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: 116770.852 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: Protein/peptide Atrial natriuretic peptide / ANP / Alpha-atrial natriuretic peptide / Alpha-hANP / Atrial natriuretic factor / ANF / CDD-ANF / ...ANP / Alpha-atrial natriuretic peptide / Alpha-hANP / Atrial natriuretic factor / ANF / CDD-ANF / CDD-ANP (99-126) / Cardionatrin / Pro atrial natriuretic factor 99-126 / proANF 99-126


Mass: 3087.505 Da / Num. of mol.: 1 / Fragment: UNP residues 124-151
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NPPA, ANP, PND / Production host: Homo sapiens (human) / References: UniProt: P01160

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Sugars , 3 types, 5 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 1 types, 2 molecules

#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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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

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 51.13 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 964634 / Symmetry type: POINT

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