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- EMDB-26692: Cardiac amyloid fibrils extracted from a variant ATTR P24S amyloi... -

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Basic information

Entry
Database: EMDB / ID: EMD-26692
TitleCardiac amyloid fibrils extracted from a variant ATTR P24S amyloidosis patient
Map datamain map for model building
Sample
  • Tissue: cardiac amyloid fibril of variant P24S transthyretin amyloidosis
    • Protein or peptide: Transthyretin
KeywordsTransthyretin / Amyloidosis / Systemic amyloidosis / ATTR / Cardiac / PROTEIN FIBRIL
Function / homology
Function and homology information


Defective visual phototransduction due to STRA6 loss of function / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / hormone binding / Non-integrin membrane-ECM interactions / molecular sequestering activity / Retinoid metabolism and transport / retinoid metabolic process / azurophil granule lumen / Amyloid fiber formation ...Defective visual phototransduction due to STRA6 loss of function / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / hormone binding / Non-integrin membrane-ECM interactions / molecular sequestering activity / Retinoid metabolism and transport / retinoid metabolic process / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / protein-containing complex binding / protein-containing complex / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Transthyretin, conserved site / Transthyretin signature 2. / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin / Transthyretin/hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsNguyen BA / Saelices L
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)1DP2HL163810-01 United States
American Heart Association847236 United States
CitationJournal: Structure / Year: 2026
Title: A shared amyloid fold in cardiac fibrils from three neuropathy-associated ATTR variants.
Authors: Maria Del Carmen Fernandez-Ramirez / Shumaila Afrin / Binh An Nguyen / Virender Singh / Maja Pękala / Preeti Singh / Yasmin Ahmed / Rose Pedretti / Andrew Lemoff / Barbara Kluve-Beckerman / ...Authors: Maria Del Carmen Fernandez-Ramirez / Shumaila Afrin / Binh An Nguyen / Virender Singh / Maja Pękala / Preeti Singh / Yasmin Ahmed / Rose Pedretti / Andrew Lemoff / Barbara Kluve-Beckerman / Farzeen Chhapra / David Eisenberg / Lorena Saelices /
Abstract: ATTR amyloidosis results from the systemic accumulation of wild-type (ATTRwt) or mutant (ATTRv) transthyretin amyloids, leading to multi-organ dysfunction and death. The disease exhibits variable ...ATTR amyloidosis results from the systemic accumulation of wild-type (ATTRwt) or mutant (ATTRv) transthyretin amyloids, leading to multi-organ dysfunction and death. The disease exhibits variable pathology and penetrance, and its relationship with the amyloid structure remains unclear. Patients carrying the neuropathy-associated variants ATTRvI84S and ATTRv-V122Δ present polymorphic ATTR fibrils, in contrast to the consistent morphology reported for most ATTR fibrils to date. Here, we aim to elucidate a potential link between neuropathic symptomatology, distinct mutations, and amyloid structural diversity, using cryo-EM. We determined the ex vivo fibril structures from the variants ATTRv-P24S, ATTRv-A25S, and ATTRv-D38A, whose patients presented variable clinical manifestations, including neuropathy. Our findings revealed that, despite differences in mutations and diverse clinical phenotypes, these variants share a common amyloid core previously identified in ATTRwt and most cardiac ATTRv. This structural consistency is significant for the development of structure-guided diagnostic tools capable of addressing the diverse spectrum of ATTR amyloidosis.
History
DepositionApr 19, 2022-
Header (metadata) releaseMay 3, 2023-
Map releaseMay 3, 2023-
UpdateOct 14, 2026-
Current statusOct 14, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26692.png

Downloads & links

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Map

FileDownload / File: emd_26692.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map for model building
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.022
Minimum - Maximum-0.1118892 - 0.18201494
Average (Standard dev.)0.0001771515 (±0.0037932992)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_26692_msk_1.map
Projections & Slices
AxesZYX

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Additional map: reconstructed map from 2 halves

Fileemd_26692_additional_1.map
Annotationreconstructed map from 2 halves
Projections & Slices
AxesZYX

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Half map: half map 1

Fileemd_26692_half_map_1.map
Annotationhalf map 1
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_26692_half_map_2.map
Annotationhalf map 2
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Sample components

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Entire : cardiac amyloid fibril of variant P24S transthyretin amyloidosis

EntireName: cardiac amyloid fibril of variant P24S transthyretin amyloidosis
Components
  • Tissue: cardiac amyloid fibril of variant P24S transthyretin amyloidosis
    • Protein or peptide: Transthyretin

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Supramolecule #1: cardiac amyloid fibril of variant P24S transthyretin amyloidosis

SupramoleculeName: cardiac amyloid fibril of variant P24S transthyretin amyloidosis
type: tissue / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human) / Organ: Heart / Tissue: Cardiac

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Macromolecule #1: Transthyretin

MacromoleculeName: Transthyretin / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
MASHRLLLLC LAGLVFVSEA GPTGTGESKC PLMVKVLDAV RGSPAINVAV HVFRKAADDT WEPFASGKTS ESGELHGLTT EEEFVEGIYK VEIDTKSYWK ALGISPFHEH AEVVFTANDS GPRRYTIAAL LSPYSYSTTA VVTNPKE

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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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / 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 / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.84 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.27 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 45958
CTF correctionSoftware - Name: RELION (ver. 3.1) / Software - details: CTFFIND-4.1 / Type: NONE
Startup modelType of model: OTHER / Details: Featureless cylinder
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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