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- EMDB-71897: Cryo-EM structure of cardiac amyloid fibril from a variant apolip... -

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Basic information

Entry
Database: EMDB / ID: EMD-71897
TitleCryo-EM structure of cardiac amyloid fibril from a variant apolipoprotein A-I R173P amyloidosis patient
Map dataprimary map for building model
Sample
  • Complex: amyloid fibrils of apoliprotein A-I amyloidosis, variant R173P from cardiac tissue
    • Protein or peptide: Apolipoprotein A-I
KeywordsApolipoprotein A-I / AApoAI / R173P / cardiac / amyloidosis. / PROTEIN FIBRIL
Function / homology
Function and homology information


Defective ABCA1 causes TGD / high-density lipoprotein particle receptor binding / peptidyl-methionine modification / HDL clearance / spherical high-density lipoprotein particle / Scavenging by Class B Receptors / negative regulation of response to cytokine stimulus / protein oxidation / regulation of intestinal cholesterol absorption / vitamin transport ...Defective ABCA1 causes TGD / high-density lipoprotein particle receptor binding / peptidyl-methionine modification / HDL clearance / spherical high-density lipoprotein particle / Scavenging by Class B Receptors / negative regulation of response to cytokine stimulus / protein oxidation / regulation of intestinal cholesterol absorption / vitamin transport / blood vessel endothelial cell migration / cholesterol import / negative regulation of heterotypic cell-cell adhesion / apolipoprotein receptor binding / apolipoprotein A-I receptor binding / ABC transporters in lipid homeostasis / negative regulation of cell adhesion molecule production / negative regulation of cytokine production involved in immune response / HDL assembly / high-density lipoprotein particle binding / negative regulation of very-low-density lipoprotein particle remodeling / glucocorticoid metabolic process / acylglycerol homeostasis / phosphatidylcholine biosynthetic process / phosphatidylcholine-sterol O-acyltransferase activator activity / positive regulation of phospholipid efflux / Chylomicron remodeling / cellular response to lipoprotein particle stimulus / Chylomicron assembly / high-density lipoprotein particle clearance / phospholipid efflux / chylomicron / high-density lipoprotein particle remodeling / reverse cholesterol transport / positive regulation of cholesterol metabolic process / lipid storage / high-density lipoprotein particle assembly / phospholipid homeostasis / chemorepellent activity / lipoprotein biosynthetic process / cholesterol transfer activity / low-density lipoprotein particle / cholesterol transport / high-density lipoprotein particle / very-low-density lipoprotein particle / endothelial cell proliferation / regulation of Cdc42 protein signal transduction / HDL remodeling / cholesterol efflux / adrenal gland development / Scavenging by Class A Receptors / triglyceride homeostasis / negative regulation of interleukin-1 beta production / negative chemotaxis / cholesterol binding / cholesterol biosynthetic process / amyloid-beta formation / positive regulation of Rho protein signal transduction / positive regulation of cholesterol efflux / endocytic vesicle / negative regulation of tumor necrosis factor-mediated signaling pathway / Scavenging of heme from plasma / Retinoid metabolism and transport / cholesterol metabolic process / positive regulation of stress fiber assembly / heat shock protein binding / endocytic vesicle lumen / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of phagocytosis / cholesterol homeostasis / integrin-mediated signaling pathway / Post-translational protein phosphorylation / Heme signaling / PPARA activates gene expression / phospholipid binding / negative regulation of inflammatory response / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Platelet degranulation / extracellular vesicle / amyloid-beta binding / cytoplasmic vesicle / secretory granule lumen / blood microparticle / early endosome / protein stabilization / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / Amyloid fiber formation / receptor ligand activity / signaling receptor binding / enzyme binding / protein homodimerization activity / : / extracellular exosome / extracellular region / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Apolipoprotein A/E / : / Apolipoprotein A1/A4/E domain
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsNguyen BA / Saelices L
Funding support United States, 3 items
OrganizationGrant numberCountry
American Heart Association847236 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)DP2-HL163810 United States
Welch FoundationI-2121-20220331 United States
CitationJournal: To Be Published
Title: Structural variability of apolipoprotein A-I amyloid fibrils across organs, mutations, and clinical presentations, revealed by cryo-EM
Authors: Nguyen BA / Saelices L
History
DepositionAug 4, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71897.png

Downloads & links

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Map

FileDownload / File: emd_71897.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationprimary map for building model
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 300 pix.
= 279.6 Å		0.93 Å/pix.
x 300 pix.
= 279.6 Å		0.93 Å/pix.
x 300 pix.
= 279.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0282
Minimum - Maximum-0.108131826 - 0.2383573
Average (Standard dev.)0.0001389667 (±0.0045794337)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 279.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_71897_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: combined map from two half-maps

Fileemd_71897_additional_1.map
Annotationcombined map from two half-maps
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map 01

Fileemd_71897_half_map_1.map
Annotationhalf-map 01
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map 02

Fileemd_71897_half_map_2.map
Annotationhalf-map 02
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Sample components

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Entire : amyloid fibrils of apoliprotein A-I amyloidosis, variant R173P fr...

EntireName: amyloid fibrils of apoliprotein A-I amyloidosis, variant R173P from cardiac tissue
Components
  • Complex: amyloid fibrils of apoliprotein A-I amyloidosis, variant R173P from cardiac tissue
    • Protein or peptide: Apolipoprotein A-I

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Supramolecule #1: amyloid fibrils of apoliprotein A-I amyloidosis, variant R173P fr...

SupramoleculeName: amyloid fibrils of apoliprotein A-I amyloidosis, variant R173P from cardiac tissue
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: fibrils were extracted from cardiac tissue of a variant apolipoprotein A-I R173P amyloidosis
Source (natural)Organism: Homo sapiens (human) / Organ: heart / Tissue: heart

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Macromolecule #1: Apolipoprotein A-I

MacromoleculeName: Apolipoprotein A-I / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Organ: Heart / Tissue: Heart
Molecular weightTheoretical: 28.120637 KDa
SequenceString: DEPPQSPWDR VKDLATVYVD VLKDSGRDYV SQFEGSALGK QLNLKLLDNW DSVTSTFSKL REQLGPVTQE FWDNLEKETE GLRQEMSKD LEEVKAKVQP YLDDFQKKWQ EEMELYRQKV EPLRAELQEG ARQKLHELQE KLSPLGEEMR DRARAHVDAL R THLAPYSD ...String:
DEPPQSPWDR VKDLATVYVD VLKDSGRDYV SQFEGSALGK QLNLKLLDNW DSVTSTFSKL REQLGPVTQE FWDNLEKETE GLRQEMSKD LEEVKAKVQP YLDDFQKKWQ EEMELYRQKV EPLRAELQEG ARQKLHELQE KLSPLGEEMR DRARAHVDAL R THLAPYSD ELRQRLAARL EALKENGGAR LAEYHAKATE HLSTLSEKAK PALEDLRQGL LPVLESFKVS FLSALEEYTK KL NTQ

UniProtKB: Apolipoprotein A-I

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7 / Details: H2O containing 5 mM EDTA
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 16496 / Average exposure time: 5.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.85 Å
Applied symmetry - Helical parameters - Δ&Phi: -0.66 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 165734
CTF correctionSoftware - Name: CTFFIND / Details: RELION 4 built in CTFFIND / Type: NONE
Startup modelType of model: INSILICO MODEL
In silico model: initial model was generated using relion_helix_inimodel2d.
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9pvy


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9pvz:
Cryo-EM structure of cardiac amyloid fibril from a variant apolipoprotein A-I R173P amyloidosis patient

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