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- EMDB-44430: Full-length apo GC-A -

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Basic information

Entry
Database: EMDB / ID: EMD-44430
TitleFull-length apo GC-A
Map data
Sample
  • Complex: Atrial natriuretic peptide receptor 1 dimer
    • Protein or peptide: Atrial natriuretic peptide receptor 1
KeywordsSingle 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 / body fluid secretion / receptor guanylyl cyclase signaling pathway / 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 / body fluid secretion / receptor guanylyl cyclase signaling pathway / 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 / 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
Atrial natriuretic peptide receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.82 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_44430.png

Downloads & links

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Map

FileDownload / File: emd_44430.map.gz / Format: CCP4 / Size: 71.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.17 Å/pix.
x 266 pix.
= 576.688 Å		2.17 Å/pix.
x 266 pix.
= 576.688 Å		2.17 Å/pix.
x 266 pix.
= 576.688 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.168 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.4
Minimum - Maximum-5.746715 - 9.029233
Average (Standard dev.)-0.00040071039 (±0.10535564)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions266266266
Spacing266266266
CellA=B=C: 576.688 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_44430_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_44430_half_map_2.map
Projections & Slices
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Histogram

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

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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: all
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 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GNLTVAVVLP LANTSYPWSW ARVGPAVE L ALAQVKARPD LLPGWTVRTV LGSSENALGV CSDTAAPLAA VDLKWEHNPA VFLGPGCVY AAAPVGRFTA HWRVPLLTAG APALGFGVKD EYALTTRAGP SYAKLGDFVA ALHRRLGWER QALMLYAYR PGDEEHCFFL ...String:
GNLTVAVVLP LANTSYPWSW ARVGPAVE L ALAQVKARPD LLPGWTVRTV LGSSENALGV CSDTAAPLAA VDLKWEHNPA VFLGPGCVY AAAPVGRFTA HWRVPLLTAG APALGFGVKD EYALTTRAGP SYAKLGDFVA ALHRRLGWER QALMLYAYR PGDEEHCFFL VEGLFMRVRD RLNITVDHLE FAEDDLSHYT RLLRTMPRKG R VIYICSSP DAFRTLMLLA LEAGLCGEDY VFFHLDIFGQ SLQGGQGPAP RRPWERGDGQ DV SARQAFQ AAKIITYKDP DNPEYLEFLK QLKHLAYEQF NFTMEDGLVN TIPASFHDGL LLY IQAVTE TLAHGGTVTD GENITQRMWN RSFQGVTGYL KIDSSGDRET DFSLWDMDPE NGAF RVVLN YNGTSQELVA VSGRKLNWPL GYPPPDIPKC GFDNEDPACN QDHLSTLEVL ALVGS LSLL GILIVSFFIY RKMQLEKELA SELWRVRWED VEPSSLERHL RSAGSRLTLS GRGSNY GSL LTTEGQFQVF AKTAYYKGNL VAVKRVNRKR IELTRKVLFE LKHMRDVQNE HLTRFVG AC TDPPNICILT EYCPRGSLQD ILENESITLD WMFRYSLTND IVKGMLFLHN GAICSHGN L KSSNCVVDGR FVLKITDYGL ESFRDLDPEQ GHTVYAKKLW TAPELLRMAS PPVRGSQAG DVYSFGIILQ EIALRSGVFH VEGLDLSPKE IIERVTRGEQ PPFRPSLALQ SHLEELGLLM QRCWAEDPQ ERPPFQQIRL TLRKFNRENS SNILDNLLSR MEQYANNLEE LVEERTQAYL E EKRKAEAL LYQILPHSVA EQLKRGETVQ AEAFDSVTIY FSDIVGFTAL SAESTPMQVV TL LNDLYTC FDAVIDNFDV YKVETIGDAY MVVSGLPVRN GRLHACEVAR MALALLDAVR SFR IRHRPQ EQLRLRIGIH TGPVCAGVVG LKMPRYCLFG DTVNTASRME SNGEALKIHL SSET KAVLE EFGGFELELR GDVEMKGKGK VRTYWLLGER GSSTRG

UniProtKB: Atrial natriuretic peptide receptor 1

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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: 7.82 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 283002
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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