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- EMDB-45039: Cryo-EM structure of amyloid fibril extracted from nerve of a var... -

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Basic information

Entry
Database: EMDB / ID: EMD-45039
TitleCryo-EM structure of amyloid fibril extracted from nerve of a variant ATTR V30M amyloidosis patient
Map datause for building model
Sample
  • Complex: amyloid fibril
    • Protein or peptide: Transthyretin
KeywordsAmyloidosis / Systemic amyloidosis / ATTR / nerve / PROTEIN FIBRIL
Function / homology
Function and homology information


Defective visual phototransduction due to STRA6 loss of function / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...Defective visual phototransduction due to STRA6 loss of function / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / extracellular space / 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: 3.36 Å
AuthorsNguyen AB / Afrin S / Yakubovska A / 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: 2024
Title: ATTRv-V30M amyloid fibrils from heart and nerves exhibit structural homogeneity.
Authors: Binh An Nguyen / Shumaila Afrin / Anna Yakubovska / Virender Singh / Rose Pedretti / Parker Bassett / Maja Pekala / Jaime Vaquer Alicea / Peter Kunach / Lanie Wang / Andrew Lemoff / Barbara ...Authors: Binh An Nguyen / Shumaila Afrin / Anna Yakubovska / Virender Singh / Rose Pedretti / Parker Bassett / Maja Pekala / Jaime Vaquer Alicea / Peter Kunach / Lanie Wang / Andrew Lemoff / Barbara Kluve-Beckerman / Lorena Saelices /
Abstract: Amyloidogenic transthyretin (ATTR) amyloidosis is a systemic disease characterized by the deposition of amyloid fibrils made of transthyretin. Transthyretin is primarily produced in tetrameric form ...Amyloidogenic transthyretin (ATTR) amyloidosis is a systemic disease characterized by the deposition of amyloid fibrils made of transthyretin. Transthyretin is primarily produced in tetrameric form by the liver, but also by retinal epithelium and choroid plexus. The deposition of these fibrils in the myocardium and peripheral nerves causes cardiomyopathies and neuropathies, respectively. Using cryoelectron microscopy (cryo-EM), we investigated fibrils extracted from cardiac and nerve tissues of an ATTRv-V30M patient. We found consistent fibril structures from both tissues, similar to cardiac fibrils previously described, but different from vitreous humor fibrils of the same genotype. Our findings, along with previous ATTR fibrils structural studies, suggest a uniform fibrillar architecture across different tissues when transthyretin originates from the liver. This study advances our understanding of how deposition and production sites influence fibril structure in ATTRv-V30M amyloidosis.
History
DepositionMay 23, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45039.png

Downloads & links

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Map

FileDownload / File: emd_45039.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationuse for building model
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 256 pix.
= 242.176 Å		0.95 Å/pix.
x 256 pix.
= 242.176 Å		0.95 Å/pix.
x 256 pix.
= 242.176 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.946 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0333
Minimum - Maximum-0.13717751 - 0.2295903
Average (Standard dev.)0.00022390042 (±0.0051060463)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 242.176 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45039_msk_1.map
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Additional map: reconstructed map from 2 halves maps

Fileemd_45039_additional_1.map
Annotationreconstructed map from 2 halves maps
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Half map: half-map 1

Fileemd_45039_half_map_1.map
Annotationhalf-map 1
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Half map: half-map 2

Fileemd_45039_half_map_2.map
Annotationhalf-map 2
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Sample components

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Entire : amyloid fibril

EntireName: amyloid fibril
Components
  • Complex: amyloid fibril
    • Protein or peptide: Transthyretin

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Supramolecule #1: amyloid fibril

SupramoleculeName: amyloid fibril / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: fibrils extracted from the peripheral nerve tissue of a ATTR-V30M patient
Source (natural)Organism: Homo sapiens (human) / Tissue: Peripheral nerve

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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) / Tissue: Nerve
Molecular weightTheoretical: 13.809426 KDa
SequenceString:
GPTGTGESKC PLMVKVLDAV RGSPAINVAM HVFRKAADDT WEPFASGKTS ESGELHGLTT EEEFVEGIYK VEIDTKSYWK ALGISPFHE HAEVVFTAND SGPRRYTIAA LLSPYSYSTT AVVTNPKE

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: Milli-Q 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 / Details: Blot-force 0, blotting time 3 sec.
DetailsSample was extracted using water-based extraction method.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 8957 / Average exposure time: 4.57 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 / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 4.93 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.31 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 104108
Startup modelType of model: OTHER / Details: 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:

6sdz


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

PDB-9byn:
Cryo-EM structure of amyloid fibril extracted from nerve of a variant ATTR V30M amyloidosis patient

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