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- EMDB-59706: ATTRV20I amyloid filament from hereditary amyloidosis -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-59706
TitleATTRV20I amyloid filament from hereditary amyloidosis
Map dataSharpened map
Sample
  • Complex: Filaments
    • Protein or peptide: Transthyretin
KeywordsTransthyretin / amyloid / amyloidosis / 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: 2.6 Å
AuthorsLovestam S / Scheres SHW
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: To Be Published
Title: Cryo-EM image processing of amyloid filaments in RELION-5.1
Authors: Lovestam S / Scheres SHW
History
DepositionSep 2, 2026-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_59706.png

Downloads & links

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Map

FileDownload / File: emd_59706.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.23 Å/pix.
x 256 pix.
= 315.648 Å		1.23 Å/pix.
x 256 pix.
= 315.648 Å		1.23 Å/pix.
x 256 pix.
= 315.648 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.233 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0106
Minimum - Maximum-0.05621265 - 0.09967929
Average (Standard dev.)0.00007489224 (±0.0035341003)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 315.648 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 2

Fileemd_59706_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_59706_half_map_2.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Filaments

EntireName: Filaments
Components
  • Complex: Filaments
    • Protein or peptide: Transthyretin

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Supramolecule #1: Filaments

SupramoleculeName: Filaments / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Transthyretin

MacromoleculeName: Transthyretin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.791388 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GPTGTGESKC PLMVKVLDAI RGSPAINVAV 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
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: 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: 2.0 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: 4.84 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.23 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.1) / Number images used: 228722
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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