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- PDB-9rbw: Cryo-EM structure of ANP amyloids from left atrial appendage of a... -

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Basic information

Entry
Database: PDB / ID: 9rbw
TitleCryo-EM structure of ANP amyloids from left atrial appendage of atrial fibrillation patient - polymorph B
ComponentsAtrial natriuretic peptide
KeywordsPROTEIN FIBRIL / amyloid / cardiac amyloidosis / in vivo / aggregation
Function / homology
Function and homology information


negative regulation of collecting lymphatic vessel constriction / : / : / neuropeptide receptor binding / : / mast cell granule / response to 3-methylcholanthrene / receptor guanylyl cyclase signaling pathway / positive regulation of potassium ion export across plasma membrane / cell growth involved in cardiac muscle cell development ...negative regulation of collecting lymphatic vessel constriction / : / : / neuropeptide receptor binding / : / mast cell granule / response to 3-methylcholanthrene / receptor guanylyl cyclase signaling pathway / positive regulation of potassium ion export across plasma membrane / cell growth involved in cardiac muscle cell development / synaptic signaling via neuropeptide / cGMP biosynthetic process / 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 / neuropeptide hormone activity / hormone receptor binding / negative regulation of systemic arterial blood pressure / glycinergic synapse / cardiac muscle hypertrophy in response to stress / aortic valve morphogenesis / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / : / brush border / cellular response to angiotensin / neuropeptide signaling pathway / positive regulation of heart rate / response to muscle stretch / positive regulation of cardiac muscle contraction / cell projection / 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 / Amyloid fiber formation / signaling receptor binding / perinuclear region of cytoplasm / protein-containing complex / extracellular space / extracellular region / cytoplasm
Similarity search - Function
Natriuretic peptide, atrial type / : / Natriuretic peptide, conserved site / Atrial natriuretic peptide / Natriuretic peptides signature. / Natriuretic peptide / Natriuretic peptide
Similarity search - Domain/homology
Natriuretic peptides A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsBroggini, L. / Chaves-Sanjuan, A. / Ricagno, S.
Funding support Italy, 2items
OrganizationGrant numberCountry
Fondazione CARIPLOGJC23044 Italy
Italian Ministry of Health20207XLJB2 Italy
CitationJournal: Nat Commun / Year: 2025
Title: Structural characterization of atrial natriuretic peptide amyloid fibrils from patients with atrial fibrillation.
Authors: Luca Broggini / Marco Piccoli / Antonio Chaves-Sanjuan / Diane Marie Valérie Bonnet / Federica Cirillo / Cristina Visentin / Federica Sonzini / Paola Signorelli / Ivana Lavota / Melissa ...Authors: Luca Broggini / Marco Piccoli / Antonio Chaves-Sanjuan / Diane Marie Valérie Bonnet / Federica Cirillo / Cristina Visentin / Federica Sonzini / Paola Signorelli / Ivana Lavota / Melissa Milazzo / Simona Nonnis / Lorenzo Menicanti / Giuseppe Ciconte / Carlo Pappone / Luigi Anastasia / Stefano Ricagno /
Abstract: Isolated atrial amyloidosis (IAA) is a localized cardiac disorder characterized by atrial natriuretic peptide (ANP) amyloids deposition in the atria, linked to aging and atrial fibrillation (AF). ...Isolated atrial amyloidosis (IAA) is a localized cardiac disorder characterized by atrial natriuretic peptide (ANP) amyloids deposition in the atria, linked to aging and atrial fibrillation (AF). While monomeric ANP regulates blood pressure, its dimeric form is associated with cardiovascular conditions, including AF. The mechanistic link between ANP aggregation, IAA, and AF remains unclear. Here, we present the first high-resolution structural characterization of ANP fibrils extracted from AF patients, revealing two distinct fibril polymorphs. Both present covalent ANP dimers as building blocks but diverge in their structural architecture: one features antiparallel dimers stabilized by a single disulfide bond, while the other consists of parallel dimers bridged by two interchain disulfide bonds. These fibril morphologies were conserved across patients, suggesting a common aggregation mechanism in IAA. Overall, our findings ascribe to dimeric ANP a critical role in amyloid formation, offering promising directions for earlier detection and treatment of IAA.
History
DepositionMay 27, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Atrial natriuretic peptide
D: Atrial natriuretic peptide
B: Atrial natriuretic peptide
A: Atrial natriuretic peptide
E: Atrial natriuretic peptide
F: Atrial natriuretic peptide
G: Atrial natriuretic peptide
H: Atrial natriuretic peptide
I: Atrial natriuretic peptide
J: Atrial natriuretic peptide
K: Atrial natriuretic peptide
L: Atrial natriuretic peptide
M: Atrial natriuretic peptide
N: Atrial natriuretic peptide
O: Atrial natriuretic peptide
P: Atrial natriuretic peptide
Q: Atrial natriuretic peptide
R: Atrial natriuretic peptide
S: Atrial natriuretic peptide
T: Atrial natriuretic peptide


Theoretical massNumber of molelcules
Total (without water)57,74520
Polymers57,74520
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: 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: 2887.270 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01160
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Atrial natriuretic peptide amyloid fibrils polymorph A
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 10 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4 / Details: MilliQ H2O
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 41 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
4RELION3.1CTF correction
7Coot0.8.2model fitting
11RELION3.1classification
12RELION3.13D reconstruction
13PHENIX1.19model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 179.5 ° / Axial rise/subunit: 2.36 Å / Axial symmetry: C21
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31454 / Symmetry type: HELICAL
Atomic model buildingB value: 62.89 / Protocol: AB INITIO MODEL
RefinementHighest resolution: 3.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0033985
ELECTRON MICROSCOPYf_angle_d0.55230
ELECTRON MICROSCOPYf_dihedral_angle_d10.6011530
ELECTRON MICROSCOPYf_chiral_restr0.041455
ELECTRON MICROSCOPYf_plane_restr0.002730

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