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- EMDB-70401: amyloid fibril of recombinant transforming growth factor beta ind... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-70401
Titleamyloid fibril of recombinant transforming growth factor beta induced protein FAS1-4 domain with V624M mutation, refined using helical spacing of peripheral globular domain
Map data
Sample
  • Complex: transforming growth factor beta induced protein FAS1-4 domain with V624M mutation
    • Protein or peptide: transforming growth factor beta induced protein FAS1-4 domain
Keywordsamyloid fibril / corneal dystrophy / PROTEIN FIBRIL
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 15.2 Å
AuthorsJiang YX / Sawaya MR / Eisenberg DS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)R01 AG070895 United States
CitationJournal: To Be Published
Title: Structure of TGFBIp amyloid fibril driven by a corneal dystrophy-causing mutation
Authors: Jiang YX / Sawaya MR / Salwinski L / Ge P / Wang C / Hu CJ / Hernandez H / Boyer DR / Melo F / Eisenberg DS
History
DepositionApr 28, 2025-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70401.png

Downloads & links

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Map

FileDownload / File: emd_70401.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesY (Sec.)X (Row.)Z (Col.)
0.73 Å/pix.
x 480 pix.
= 350.4 Å		0.73 Å/pix.
x 480 pix.
= 350.4 Å		0.73 Å/pix.
x 480 pix.
= 350.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.8
Minimum - Maximum-6.2630754 - 5.4764714
Average (Standard dev.)0.037661545 (±1.0280977)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin0-800
Dimensions480480480
Spacing480480480
CellA=B=C: 350.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_70401_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_70401_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_70401_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : transforming growth factor beta induced protein FAS1-4 domain wit...

EntireName: transforming growth factor beta induced protein FAS1-4 domain with V624M mutation
Components
  • Complex: transforming growth factor beta induced protein FAS1-4 domain with V624M mutation
    • Protein or peptide: transforming growth factor beta induced protein FAS1-4 domain

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Supramolecule #1: transforming growth factor beta induced protein FAS1-4 domain wit...

SupramoleculeName: transforming growth factor beta induced protein FAS1-4 domain with V624M mutation
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: transforming growth factor beta induced protein FAS1-4 domain

MacromoleculeName: transforming growth factor beta induced protein FAS1-4 domain
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
TGTVMDVLKG DNRFSMLVAA IQSAGLTETL NREGVYTVFA PTNEAFRALP PRERSRLLGD AKELANILKY HIGDEILVSG GIGALVRLKS LQGDKLEVSL KNNVVSVNKE PVAEPDIMAT NGMVHVITNV LQPPANRPQE RGDELADSAL EIFKQA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.4
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: 47.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 15.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 4788
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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