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- EMDB-44437: Full-length GC-A bound to ANP -

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Basic information

Entry
Database: EMDB / ID: EMD-44437
TitleFull-length GC-A bound to ANP
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
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.4 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_44437.png

Downloads & links

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Map

FileDownload / File: emd_44437.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.38 Å/pix.
x 192 pix.
= 456.96 Å		2.38 Å/pix.
x 192 pix.
= 456.96 Å		2.38 Å/pix.
x 192 pix.
= 456.96 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.38 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-1.231994 - 2.9250853
Average (Standard dev.)0.00013020428 (±0.08186253)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 456.96002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_44437_half_map_1.map
Projections & Slices
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Density Histograms

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Histogram (log scale)

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Half map: #2

Fileemd_44437_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)
SequenceString: DYKDDDDKAA A GNLTVAVV LPLANTSYPW SWARVGPAVE LALAQVKAR PDLLPGWTVR TVLGSSENAL GVCSDTAAPL AAVDLKWEHN PAVFLGPGCV Y AAAPVGRF TAHWRVPLLT AGAPALGFGV KDEYALTTRA GPSYAKLGDF VAALHRRLGW ER QALMLYA ...String:
DYKDDDDKAA A GNLTVAVV LPLANTSYPW SWARVGPAVE LALAQVKAR PDLLPGWTVR TVLGSSENAL GVCSDTAAPL AAVDLKWEHN PAVFLGPGCV Y AAAPVGRF TAHWRVPLLT AGAPALGFGV KDEYALTTRA GPSYAKLGDF VAALHRRLGW ER QALMLYA YRPGDEEHCF FLVEGLFMRV RDRLNITVDH LEFAEDDLSH YTRLLRTMPR KGR VIYICS SPDAFRTLML LALEAGLCGE DYVFFHLDIF GQSLQGGQGP APRRPWERGD GQDV SARQA FQAAKIITYK DPDNPEYLEF LKQLKHLAYE QFNFTMEDGL VNTIPASFHD GLLLY IQAV TETLAHGGTV TDGENITQRM WNRSFQGVTG YLKIDSSGDR ETDFSLWDMD PENGAF RVV LNYNGTSQEL VAVSGRKLNW PLGYPPPDIP KCGFDNEDPA CNQDHLSTLE VLALVGS LS LLGILIVSFF IYRKMQLEKE LASELWRVRW EDVEPSSLER HLRSAGSRLT LSGRGSNY G SLLTTEGQFQ VFAKTAYYKG NLVAVKRVNR KRIELTRKVL FELKHMRDVQ NEHLTRFVG ACTDPPNICI LTEYCPRGSL QDILENESIT LDWMFRYSLT NDIVKGMLFL HNGAICSHGN LKSSNCVVD GRFVLKITDY GLESFRDLDP EQGHTVYAKK LWTAPELLRM ASPPVRGSQA G DVYSFGII LQEIALRSGV FHVEGLDLSP KEIIERVTRG EQPPFRPSLA LQSHLEELGL LM QRCWAED PQERPPFQQI RLTLRKFNRE NSSNILDNLL SRMEQYANNL EELVEERTQA YLE EKRKAE ALLYQILPHS VAEQLKRGET VQAEAFDSVT IYFSDIVGFT ALSAESTPMQ VVTL LNDLY TCFDAVIDNF DVYKVETIGD AYMVVSGLPV RNGRLHACEV ARMALALLDA VRSFR IRHR PQEQLRLRIG IHTGPVCAGV VGLKMPRYCL FGDTVNTASR MESNGEALKI HLSSET KAV LEEFGGFELE LRGDVEMKGK GKVRTYWLLG ERGSSTRG

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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

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12270
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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