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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 / : / 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: 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: 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 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

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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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