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- EMDB-53910: Cryo-EM structure of ANP amyloids from left atrial appendage of a... -

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Basic information

Entry
Database: EMDB / ID: EMD-53910
TitleCryo-EM structure of ANP amyloids from left atrial appendage of atrial fibrillation patient - polymorph B
Map data
Sample
  • Complex: Atrial natriuretic peptide amyloid fibrils polymorph A
    • Protein or peptide: Atrial natriuretic peptide
Keywordsamyloid / cardiac amyloidosis / in vivo / aggregation / PROTEIN FIBRIL
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)
Methodhelical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsBroggini L / Chaves-Sanjuan A / Ricagno S
Funding support Italy, 2 items
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, 2025-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53910.png

Downloads & links

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Map

FileDownload / File: emd_53910.map.gz / Format: CCP4 / Size: 244.1 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.)
0.84 Å/pix.
x 400 pix.
= 335.472 Å		0.84 Å/pix.
x 400 pix.
= 335.472 Å		0.84 Å/pix.
x 400 pix.
= 335.472 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83868 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.017
Minimum - Maximum-0.039912924 - 0.061980553
Average (Standard dev.)0.00005765527 (±0.0011996385)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 335.47162 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53910_msk_1.map
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Half map: Half map 1

Fileemd_53910_half_map_1.map
AnnotationHalf map 1
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Half map: Half map 2

Fileemd_53910_half_map_2.map
AnnotationHalf map 2
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Sample components

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Entire : Atrial natriuretic peptide amyloid fibrils polymorph A

EntireName: Atrial natriuretic peptide amyloid fibrils polymorph A
Components
  • Complex: Atrial natriuretic peptide amyloid fibrils polymorph A
    • Protein or peptide: Atrial natriuretic peptide

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Supramolecule #1: Atrial natriuretic peptide amyloid fibrils polymorph A

SupramoleculeName: Atrial natriuretic peptide amyloid fibrils polymorph A
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10 kDa/nm

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Macromolecule #1: Atrial natriuretic peptide

MacromoleculeName: Atrial natriuretic peptide / type: protein_or_peptide / ID: 1 / Number of copies: 20 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 2.88727 KDa
SequenceString:
RRSSCFGGRM DRIGAQSGLG CNSFRY

UniProtKB: Natriuretic peptides A

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.4 / Details: MilliQ H2O
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 41.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.36 Å
Applied symmetry - Helical parameters - Δ&Phi: 179.5 °
Applied symmetry - Helical parameters - Axial symmetry: C21 (21 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 31454
CTF correctionSoftware - Name: RELION (ver. 3.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Ab initio model
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL / Overall B value: 62.89
Output model

PDB-9rbw:
Cryo-EM structure of ANP amyloids from left atrial appendage of atrial fibrillation patient - polymorph B

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