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- EMDB-53891: Cryo-EM structure of ANP amyloids from left atrial appendage of a... -

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Basic information

Entry
Database: EMDB / ID: EMD-53891
TitleCryo-EM structure of ANP amyloids from left atrial appendage of atrial fibrillation patient - polymorph A
Map data
Sample
  • Complex: Atrial natriuretic peptide amyloid fibrils polymorph A
    • Protein or peptide: Natriuretic peptides A
Keywordsamyloid / cardiac amyloidosis / in vivo / aggregation / PROTEIN FIBRIL
Function / homology
Function and homology information


negative regulation of collecting lymphatic vessel constriction / : / positive regulation of cGMP-mediated signaling / neuropeptide receptor binding / regulation of high voltage-gated calcium channel activity / mast cell granule / response to 3-methylcholanthrene / receptor guanylyl cyclase signaling pathway / positive regulation of potassium ion export across plasma membrane / synaptic signaling via neuropeptide ...negative regulation of collecting lymphatic vessel constriction / : / positive regulation of cGMP-mediated signaling / neuropeptide receptor binding / regulation of high voltage-gated calcium channel activity / mast cell granule / response to 3-methylcholanthrene / receptor guanylyl cyclase signaling pathway / positive regulation of potassium ion export across plasma membrane / synaptic signaling via neuropeptide / cell growth involved in cardiac muscle cell development / 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 / glycinergic synapse / negative regulation of systemic arterial blood pressure / cardiac muscle hypertrophy in response to stress / aortic valve morphogenesis / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / cGMP-mediated signaling / 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 / female pregnancy / cellular response to mechanical stimulus / 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: 2.96 Å
AuthorsBroggini L / Chaves-Sanjuan A / Ricagno S
Funding support Italy, 2 items
OrganizationGrant numberCountry
Fondazione CARIPLOGJC23044 Italy
Italian Ministry of Health20207XLJB2 Italy
CitationJournal: To Be Published
Title: Structural characterization of atrial natriuretic peptide amyloid fibrils from patients with atrial fibrillation
Authors: Broggini L / Piccoli M / Chaves-Sanjuan A / Bonnet DM / Cirillo F / Visentin C / Sonzini F / Signorelli P / Lavota I / Milazzo M / Nonnis S / Menicanti L / Ciconte G / Pappone C / Anastasia L / Ricagno S
History
DepositionMay 22, 2025-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: PDBe / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_53891.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.83868 Å
Density
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.027862797 - 0.056477174
Average (Standard dev.)0.000053028714 (±0.0010144545)
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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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: Natriuretic peptides A

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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: Natriuretic peptides A

MacromoleculeName: Natriuretic peptides A / type: protein_or_peptide / ID: 1 / Number of copies: 20 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 2.572882 KDa
SequenceString:
SSCFGGRMDR IGAQSGLGCN SFRY

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 reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 2.35 Å
Applied symmetry - Helical parameters - Δ&Phi: 178.9 °
Applied symmetry - Helical parameters - Axial symmetry: C21 (21 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 67547
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

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL / Overall B value: 73.85
Output model

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

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