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- EMDB-44434: Extracellular domain of GC-A bound to ANP -

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Basic information

Entry
Database: EMDB / ID: EMD-44434
TitleExtracellular domain of GC-A bound to ANP
Map data
Sample
  • Complex: Atrial natriuretic peptide receptor 1 dimer
    • Protein or peptide: Atrial natriuretic peptide receptor 1
    • Protein or peptide: Atrial natriuretic peptide
  • Ligand: CHLORIDE ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSingle pass transmembrane protein / guanylyl cyclase / atrial natriuretic peptide receptor / hypertension / membrane protein / LYASE
Function / homology
Function and homology information


negative regulation of collecting lymphatic vessel constriction / : / ANPR-A receptor complex / natriuretic peptide receptor activity / : / neuropeptide receptor binding / : / mast cell granule / response to 3-methylcholanthrene / body fluid secretion ...negative regulation of collecting lymphatic vessel constriction / : / ANPR-A receptor complex / natriuretic peptide receptor activity / : / neuropeptide receptor binding / : / mast cell granule / response to 3-methylcholanthrene / body fluid secretion / receptor guanylyl cyclase signaling pathway / positive regulation of potassium ion export across plasma membrane / peptide receptor activity / positive regulation of renal sodium excretion / guanylate cyclase / cell growth involved in cardiac muscle cell development / synaptic signaling via neuropeptide / cGMP biosynthetic process / guanylate cyclase activity / negative regulation of JUN kinase activity / regulation of atrial cardiac muscle cell membrane repolarization / Physiological factors / cardiac conduction system development / YAP1- and WWTR1 (TAZ)-stimulated gene expression / sodium ion export across plasma membrane / regulation of vascular permeability / neuropeptide hormone activity / positive regulation of urine volume / hormone receptor binding / negative regulation of systemic arterial blood pressure / glycinergic synapse / cardiac muscle hypertrophy in response to stress / G protein-coupled peptide receptor activity / aortic valve morphogenesis / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / : / dopamine metabolic process / hormone binding / peptide hormone binding / brush border / cellular response to angiotensin / neuropeptide signaling pathway / positive regulation of heart rate / response to muscle stretch / positive regulation of cardiac muscle contraction / negative regulation of angiogenesis / blood vessel diameter maintenance / cell projection / negative regulation of smooth muscle cell proliferation / cellular response to mechanical stimulus / female pregnancy / negative regulation of cell growth / response to insulin / hormone activity / regulation of blood pressure / vasodilation / cellular response to hydrogen peroxide / protein folding / : / perikaryon / response to hypoxia / cell surface receptor signaling pathway / receptor complex / protein kinase activity / Amyloid fiber formation / signaling receptor binding / GTP binding / perinuclear region of cytoplasm / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsLiu S / Huang X
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM138676 United States
CitationJournal: Nat Struct Mol Biol / Year: 2025
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, 2024-
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44434.png

Downloads & links

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Map

FileDownload / File: emd_44434.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 160 pix.
= 173.216 Å		1.08 Å/pix.
x 160 pix.
= 173.216 Å		1.08 Å/pix.
x 160 pix.
= 173.216 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-3.7221117 - 6.0368786
Average (Standard dev.)0.004908656 (±0.22351399)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 173.216 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_44434_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_44434_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Atrial natriuretic peptide receptor 1 dimer

EntireName: Atrial natriuretic peptide receptor 1 dimer
Components
  • Complex: Atrial natriuretic peptide receptor 1 dimer
    • Protein or peptide: Atrial natriuretic peptide receptor 1
    • Protein or peptide: Atrial natriuretic peptide
  • Ligand: CHLORIDE ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Atrial natriuretic peptide receptor 1 dimer

SupramoleculeName: Atrial natriuretic peptide receptor 1 dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Atrial natriuretic peptide receptor 1

MacromoleculeName: Atrial natriuretic peptide receptor 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: guanylate cyclase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 116.770852 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DYKDDDDKAA AGNLTVAVVL PLANTSYPWS WARVGPAVEL ALAQVKARPD LLPGWTVRTV LGSSENALGV CSDTAAPLAA VDLKWEHNP AVFLGPGCVY AAAPVGRFTA HWRVPLLTAG APALGFGVKD EYALTTRAGP SYAKLGDFVA ALHRRLGWER Q ALMLYAYR ...String:
DYKDDDDKAA AGNLTVAVVL PLANTSYPWS WARVGPAVEL ALAQVKARPD LLPGWTVRTV LGSSENALGV CSDTAAPLAA VDLKWEHNP AVFLGPGCVY AAAPVGRFTA HWRVPLLTAG APALGFGVKD EYALTTRAGP SYAKLGDFVA ALHRRLGWER Q ALMLYAYR PGDEEHCFFL VEGLFMRVRD RLNITVDHLE FAEDDLSHYT RLLRTMPRKG RVIYICSSPD AFRTLMLLAL EA GLCGEDY VFFHLDIFGQ SLQGGQGPAP RRPWERGDGQ DVSARQAFQA AKIITYKDPD NPEYLEFLKQ LKHLAYEQFN FTM EDGLVN TIPASFHDGL LLYIQAVTET LAHGGTVTDG ENITQRMWNR SFQGVTGYLK IDSSGDRETD FSLWDMDPEN GAFR VVLNY NGTSQELVAV SGRKLNWPLG YPPPDIPKCG FDNEDPACNQ DHLSTLEVLA LVGSLSLLGI LIVSFFIYRK MQLEK ELAS ELWRVRWEDV EPSSLERHLR SAGSRLTLSG RGSNYGSLLT TEGQFQVFAK TAYYKGNLVA VKRVNRKRIE LTRKVL FEL KHMRDVQNEH LTRFVGACTD PPNICILTEY CPRGSLQDIL ENESITLDWM FRYSLTNDIV KGMLFLHNGA ICSHGNL KS SNCVVDGRFV LKITDYGLES FRDLDPEQGH TVYAKKLWTA PELLRMASPP VRGSQAGDVY SFGIILQEIA LRSGVFHV E GLDLSPKEII ERVTRGEQPP FRPSLALQSH LEELGLLMQR CWAEDPQERP PFQQIRLTLR KFNRENSSNI LDNLLSRME QYANNLEELV EERTQAYLEE KRKAEALLYQ ILPHSVAEQL KRGETVQAEA FDSVTIYFSD IVGFTALSAE STPMQVVTLL NDLYTCFDA VIDNFDVYKV ETIGDAYMVV SGLPVRNGRL HACEVARMAL ALLDAVRSFR IRHRPQEQLR LRIGIHTGPV C AGVVGLKM PRYCLFGDTV NTASRMESNG EALKIHLSSE TKAVLEEFGG FELELRGDVE MKGKGKVRTY WLLGERGSST RG

UniProtKB: Atrial natriuretic peptide receptor 1

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Macromolecule #2: Atrial natriuretic peptide

MacromoleculeName: Atrial natriuretic peptide / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.087505 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SLRRSSCFGG RMDRIGAQSG LGCNSFRY

UniProtKB: Natriuretic peptides A

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Macromolecule #5: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.13 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 964634
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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