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- EMDB-52457: Amyloid fibril of apolipoprotein A-IV -

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Basic information

Entry
Database: EMDB / ID: EMD-52457
TitleAmyloid fibril of apolipoprotein A-IV
Map dataCombined half-maps with helical symmetry imposed
Sample
  • Complex: Amyloid fibril of apolipoprotein A-IV
    • Protein or peptide: Apolipoprotein A-IV
KeywordsAmyloid / Apolipoprotein / Fibril / PROTEIN FIBRIL
Function / homology
Function and homology information


protein-lipid complex assembly / response to triglyceride / chylomicron assembly / negative regulation of plasma lipoprotein oxidation / positive regulation of triglyceride catabolic process / response to lipid hydroperoxide / chylomicron remodeling / response to stilbenoid / peripheral nervous system axon regeneration / Assembly of active LPL and LIPC lipase complexes ...protein-lipid complex assembly / response to triglyceride / chylomicron assembly / negative regulation of plasma lipoprotein oxidation / positive regulation of triglyceride catabolic process / response to lipid hydroperoxide / chylomicron remodeling / response to stilbenoid / peripheral nervous system axon regeneration / Assembly of active LPL and LIPC lipase complexes / regulation of cholesterol transport / regulation of intestinal cholesterol absorption / phosphatidylcholine metabolic process / acylglycerol homeostasis / very-low-density lipoprotein particle remodeling / phosphatidylcholine-sterol O-acyltransferase activator activity / Chylomicron remodeling / lipid transporter activity / Chylomicron assembly / lipoprotein metabolic process / phospholipid efflux / chylomicron / positive regulation of fatty acid biosynthetic process / high-density lipoprotein particle remodeling / reverse cholesterol transport / phosphatidylcholine binding / low-density lipoprotein particle / cholesterol transfer activity / high-density lipoprotein particle / very-low-density lipoprotein particle / cholesterol efflux / leukocyte cell-cell adhesion / lipid transport / antioxidant activity / lipid homeostasis / cholesterol metabolic process / Retinoid metabolism and transport / lipid catabolic process / removal of superoxide radicals / cholesterol homeostasis / innate immune response in mucosa / hydrogen peroxide catabolic process / phospholipid binding / extracellular vesicle / : / blood microparticle / early endosome / endoplasmic reticulum lumen / Amyloid fiber formation / copper ion binding / synapse / lipid binding / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / 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: 3.3 Å
AuthorsAibara S / Kassner A / Wong E / Klingel K / Papworth M / Althage M / Wang QD / Correia C / Milting H / Oliveira TM
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Apolipoprotein A-IV fibrils: structural diagnosis of mixed cardiac amyloidosis.
Authors: Shintaro Aibara / Astrid Kassner / Edmond Wong / Karin Klingel / Monika Papworth / Magnus Althage / Qing-Dong Wang / Claudia Correia / Hendrik Milting / Taiana Maia de Oliveira /
Abstract: Cardiac amyloidosis (CA) occurs when misfolded proteins deposit as fibrils in the extracellular space of the heart. The fibrillogenic properties of apolipoprotein A-IV (ApoAIV) have been ...Cardiac amyloidosis (CA) occurs when misfolded proteins deposit as fibrils in the extracellular space of the heart. The fibrillogenic properties of apolipoprotein A-IV (ApoAIV) have been histologically observed and associated with CA pathogenesis. We report the structure of an ApoAIV amyloid from a patient's heart, which coexist amongst transthyretin (TTR) amyloids. These cases of undetected mixed CA highlight the importance of developing broad-spectrum anti-amyloid treatments to improve outcomes in patients.
History
DepositionJan 6, 2025-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52457.png

Downloads & links

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Map

FileDownload / File: emd_52457.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCombined half-maps with helical symmetry imposed
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.28 Å/pix.
x 180 pix.
= 230.4 Å		1.28 Å/pix.
x 180 pix.
= 230.4 Å		1.28 Å/pix.
x 180 pix.
= 230.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.28 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.027583383 - 0.053384975
Average (Standard dev.)0.00032184008 (±0.0033645127)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 230.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unbinned half map 2

Fileemd_52457_additional_1.map
AnnotationUnbinned half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unbinned half map 1

Fileemd_52457_additional_2.map
AnnotationUnbinned half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unbinned map with helical symmetry imposed (b-factor -60)

Fileemd_52457_additional_3.map
AnnotationUnbinned map with helical symmetry imposed (b-factor -60)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1

Fileemd_52457_half_map_1.map
AnnotationHalf-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2

Fileemd_52457_half_map_2.map
AnnotationHalf-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Amyloid fibril of apolipoprotein A-IV

EntireName: Amyloid fibril of apolipoprotein A-IV
Components
  • Complex: Amyloid fibril of apolipoprotein A-IV
    • Protein or peptide: Apolipoprotein A-IV

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Supramolecule #1: Amyloid fibril of apolipoprotein A-IV

SupramoleculeName: Amyloid fibril of apolipoprotein A-IV / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Apolipoprotein A-IV

MacromoleculeName: Apolipoprotein A-IV / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.433961 KDa
SequenceString: MFLKAVVLTL ALVAVAGARA EVSADQVATV MWDYFSQLSN NAKEAVEHLQ KSELTQQLNA LFQDKLGEVN TYAGDLQKKL VPFATELHE RLAKDSEKLK EEIGKELEEL RARLLPHANE VSQKIGDNLR ELQQRLEPYA DQLRTQVSTQ AEQLRRQLTP Y AQRMERVL ...String:
MFLKAVVLTL ALVAVAGARA EVSADQVATV MWDYFSQLSN NAKEAVEHLQ KSELTQQLNA LFQDKLGEVN TYAGDLQKKL VPFATELHE RLAKDSEKLK EEIGKELEEL RARLLPHANE VSQKIGDNLR ELQQRLEPYA DQLRTQVSTQ AEQLRRQLTP Y AQRMERVL RENADSLQAS LRPHADELKA KIDQNVEELK GRLTPYADEF KVKIDQTVEE LRRSLAPYAQ DTQEKLNHQL EG LTFQMKK NAEELKARIS ASAEELRQRL APLAEDVRGN LRGNTEGLQK SLAELGGHLD QQVEEFRRRV EPYGENFNKA LVQ QMEQLR QKLGPHAGDV EGHLSFLEKD LRDKVNSFFS TFKEKESQDK TLSLPELEQQ QEQQQEQQQE QVQMLAPLES

UniProtKB: Apolipoprotein A-IV

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 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: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.76 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.04 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 36124
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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