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

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Basic information

Entry
Database: PDB / ID: 9rbd
TitleCryo-EM structure of ANP amyloids from left atrial appendage of atrial fibrillation patient - polymorph A
ComponentsNatriuretic peptides A
KeywordsPROTEIN FIBRIL / amyloid / cardiac amyloidosis / in vivo / aggregation
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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsBroggini, L. / Chaves-Sanjuan, A. / Ricagno, S.
Funding support Italy, 2items
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, D.M. / Cirillo, F. / Visentin, C. / Sonzini, F. / Signorelli, P. / Lavota, I. / Milazzo, M. / Nonnis, S. / Menicanti, L. / Ciconte, ...Authors: Broggini, L. / Piccoli, M. / Chaves-Sanjuan, A. / Bonnet, D.M. / 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, 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: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
J: Natriuretic peptides A
L: Natriuretic peptides A
g: Natriuretic peptides A
i: Natriuretic peptides A
A: Natriuretic peptides A
B: Natriuretic peptides A
C: Natriuretic peptides A
D: Natriuretic peptides A
E: Natriuretic peptides A
F: Natriuretic peptides A
G: Natriuretic peptides A
H: Natriuretic peptides A
I: Natriuretic peptides A
K: Natriuretic peptides A
M: Natriuretic peptides A
N: Natriuretic peptides A
O: Natriuretic peptides A
P: Natriuretic peptides A
Q: Natriuretic peptides A
R: Natriuretic peptides A


Theoretical massNumber of molelcules
Total (without water)51,45820
Polymers51,45820
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
Natriuretic peptides A / Atrial natriuretic factor prohormone / proANF / Atrial natriuretic peptide prohormone / preproANP / ...Atrial natriuretic factor prohormone / proANF / Atrial natriuretic peptide prohormone / preproANP / proANP / Atriopeptigen / Cardiodilatin / CDD / preproCDD-ANF


Mass: 2572.882 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: 178.9 ° / Axial rise/subunit: 2.35 Å / Axial symmetry: C21
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 67547 / Num. of class averages: 1 / Symmetry type: HELICAL
Atomic model buildingB value: 73.85 / Protocol: AB INITIO MODEL

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