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- EMDB-44433: Kinase homology domain of apo GC-A -

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Basic information

Entry
Database: EMDB / ID: EMD-44433
TitleKinase homology domain of apo GC-A
Map data
Sample
  • Complex: Atrial natriuretic peptide receptor 1 dimer
    • Protein or peptide: Atrial natriuretic peptide receptor 1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: water
KeywordsSingle pass transmembrane protein / guanylyl cyclase / atrial natriuretic peptide receptor / hypertension / membrane protein / LYASE
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
Atrial natriuretic peptide receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 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: 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, 2024-
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44433.png

Downloads & links

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Map

FileDownload / File: emd_44433.map.gz / Format: CCP4 / Size: 64 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.)
1.08 Å/pix.
x 256 pix.
= 277.504 Å		1.08 Å/pix.
x 256 pix.
= 277.504 Å		1.08 Å/pix.
x 256 pix.
= 277.504 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.084 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-2.222411 - 2.9331515
Average (Standard dev.)0.0016971352 (±0.058153357)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 277.504 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_44433_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_44433_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
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: water

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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
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: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 183052
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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