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- EMDB-74399: Cryo-EM structure of hepatic amyloid fibril from a variant ATTRV1... -

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Basic information

Entry
Database: EMDB / ID: EMD-74399
TitleCryo-EM structure of hepatic amyloid fibril from a variant ATTRV122delta, single filament morphology
Map dataprimary map
Sample
  • Complex: fibrils of ATTRV122delta
    • Protein or peptide: Transthyretin
KeywordsATTR / Systemic amyloidosis / V122delta / amyloid / PROTEIN FIBRIL
Function / homology
Function and homology information


Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / hormone binding / Non-integrin membrane-ECM interactions / phototransduction, visible light / molecular sequestering activity / retinoid metabolic process / Retinoid metabolism and transport ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / hormone binding / Non-integrin membrane-ECM interactions / phototransduction, visible light / molecular sequestering activity / retinoid metabolic process / Retinoid metabolism and transport / hormone activity / 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: 2.9 Å
AuthorsNguyen BA / Ahmed Y / Saelices L
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)DP2-HL163810 United States
American Heart Association847236 United States
Welch FoundationI-2121-20220331 United States
CitationJournal: Commun Biol / Year: 2026
Title: Amyloid fibril polymorphism in the heart and liver of a patient with polyneuropathic ATTRv-V122Δ amyloidosis.
Authors: Yasmin Ahmed / Binh An Nguyen / Candace Kelly / Shumaila Afrin / Virender Singh / Bret M Evers / John M Shelton / Christian Lopez Escobar / Preeti Singh / Rose Pedretti / Lanie Wang / Parker ...Authors: Yasmin Ahmed / Binh An Nguyen / Candace Kelly / Shumaila Afrin / Virender Singh / Bret M Evers / John M Shelton / Christian Lopez Escobar / Preeti Singh / Rose Pedretti / Lanie Wang / Parker Bassett / Maria Del Carmen Fernandez-Ramirez / Maja Pekala / Andrew Lemoff / Barbara Kluve-Beckerman / Lorena Saelices /
Abstract: ATTR amyloidosis is a phenotypically heterogeneous disease characterized by the pathological deposition of transthyretin in the form of amyloid fibrils into various organs. ATTR amyloidosis may ...ATTR amyloidosis is a phenotypically heterogeneous disease characterized by the pathological deposition of transthyretin in the form of amyloid fibrils into various organs. ATTR amyloidosis may result from mutations in variant (ATTRv) amyloidosis, or aging in wild-type (ATTRwt) amyloidosis. ATTRwt generally manifests as cardiomyopathy, whereas ATTRv may present as polyneuropathy, cardiomyopathy, or mixed, in combination with many other symptoms deriving from multisystem organ involvement. Over 220 different mutational variants of transthyretin have been identified, many of them being linked to specific disease symptoms. Yet, the role of these mutations in explaining differential disease manifestations remains unclear. Using cryo-electron microscopy, here we structurally characterized fibrils from the heart and the liver of an ATTRv patient carrying the V122∆ mutation, which is predominantly associated with polyneuropathy. Our results show that these fibrils are polymorphic, presenting as both single and double filaments. Our study alludes to a structural connection contributing to phenotypic variation in ATTR amyloidosis, as polymorphism in ATTR fibrils may manifest in patients with predominantly polyneuropathic phenotypes.
History
DepositionDec 8, 2025-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74399.png

Downloads & links

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Map

FileDownload / File: emd_74399.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationprimary map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 247.8 Å		0.83 Å/pix.
x 300 pix.
= 247.8 Å		0.83 Å/pix.
x 300 pix.
= 247.8 Å

Surface

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Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00717
Minimum - Maximum-0.028608039 - 0.04895399
Average (Standard dev.)0.000049357666 (±0.0011770006)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 247.79999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_74399_msk_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: Combined map from the two half-maps

Fileemd_74399_additional_1.map
AnnotationCombined map from the two half-maps
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Half map: half-map1

Fileemd_74399_half_map_1.map
Annotationhalf-map1
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Half map: half-map2

Fileemd_74399_half_map_2.map
Annotationhalf-map2
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Sample components

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Entire : fibrils of ATTRV122delta

EntireName: fibrils of ATTRV122delta
Components
  • Complex: fibrils of ATTRV122delta
    • Protein or peptide: Transthyretin

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Supramolecule #1: fibrils of ATTRV122delta

SupramoleculeName: fibrils of ATTRV122delta / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: fibril extracted from the liver, postmortem.
Source (natural)Organism: Homo sapiens (human) / Organ: Liver / Tissue: Liver

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Macromolecule #1: Transthyretin

MacromoleculeName: Transthyretin / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Organ: Liver / Tissue: Liver
Molecular weightTheoretical: 13.678229 KDa
SequenceString:
GPTGTGESKC PLMVKVLDAV RGSPAINVAV HVFRKAADDT WEPFASGKTS ESGELHGLTT EEEFVEGIYK VEIDTKSYWK ALGISPFHE HAEVVFTAND SGPRRYTIAA LLSPYSYSTT AVTNPKE

UniProtKB: Transthyretin

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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: ice-chilled water
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
Detailsfibrils were extracted from cardiac tissue using a water-based extraction method.

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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: 4366 / Average exposure time: 2.06 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.82 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.19 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 21384
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING ONLY
Segment selectionNumber selected: 345559 / Software - Name: RELION (ver. 4.0)
Details: Initial segment after extraction at box size of 300 pixel
Startup modelType of model: INSILICO MODEL / In silico model: featureless cylinder
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:

8bdm


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 49.97
Output model

PDB-9zld:
Cryo-EM structure of hepatic amyloid fibril from a variant ATTRV122delta, single filament morphology

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