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- EMDB-5590: Electron cryo-microscopy of a cross-beta amyloid fibril polymorph -

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Basic information

Entry
Database: EMDB / ID: EMD-5590
TitleElectron cryo-microscopy of a cross-beta amyloid fibril polymorph
Map dataReconstruction of doublet cross-beta amyloid fibril polymorph
Sample
  • Sample: Doublet cross-beta amyloid fibril polymorph
  • Protein or peptide: Transthyretin(105-115)
Keywordsamyloid fibrils / cross-beta structure / protein aggregation / polymorphism
Function / homology
Function and homology information


The canonical retinoid cycle in rods (twilight vision) / Retinoid metabolism and transport / thyroid hormone metabolic process / hormone binding / Neutrophil degranulation / thyroid hormone binding / purine nucleobase metabolic process / hormone activity / protein-containing complex binding / protein-containing complex ...The canonical retinoid cycle in rods (twilight vision) / Retinoid metabolism and transport / thyroid hormone metabolic process / hormone binding / Neutrophil degranulation / thyroid hormone binding / purine nucleobase metabolic process / hormone activity / protein-containing complex binding / protein-containing complex / extracellular space / 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 speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.7 Å
AuthorsFitzpatrick AWP / Debelouchina GT / Bayro MJ / Clare DK / Caporini MA / Bajaj VS / Jaroniec CP / Wang L / Ladizhansky V / Muller S ...Fitzpatrick AWP / Debelouchina GT / Bayro MJ / Clare DK / Caporini MA / Bajaj VS / Jaroniec CP / Wang L / Ladizhansky V / Muller S / MacPhee CE / Waudby CA / Mott HR / De-Simone A / Knowles TPJ / Saibil HR / Vendruscolo M / Orlova EV / Griffin RG / Dobson CM
CitationJournal: Proc Natl Acad Sci U S A / Year: 2013
Title: Atomic structure and hierarchical assembly of a cross-β amyloid fibril.
Authors: Anthony W P Fitzpatrick / Galia T Debelouchina / Marvin J Bayro / Daniel K Clare / Marc A Caporini / Vikram S Bajaj / Christopher P Jaroniec / Luchun Wang / Vladimir Ladizhansky / Shirley A ...Authors: Anthony W P Fitzpatrick / Galia T Debelouchina / Marvin J Bayro / Daniel K Clare / Marc A Caporini / Vikram S Bajaj / Christopher P Jaroniec / Luchun Wang / Vladimir Ladizhansky / Shirley A Müller / Cait E MacPhee / Christopher A Waudby / Helen R Mott / Alfonso De Simone / Tuomas P J Knowles / Helen R Saibil / Michele Vendruscolo / Elena V Orlova / Robert G Griffin / Christopher M Dobson /
Abstract: The cross-β amyloid form of peptides and proteins represents an archetypal and widely accessible structure consisting of ordered arrays of β-sheet filaments. These complex aggregates have ...The cross-β amyloid form of peptides and proteins represents an archetypal and widely accessible structure consisting of ordered arrays of β-sheet filaments. These complex aggregates have remarkable chemical and physical properties, and the conversion of normally soluble functional forms of proteins into amyloid structures is linked to many debilitating human diseases, including several common forms of age-related dementia. Despite their importance, however, cross-β amyloid fibrils have proved to be recalcitrant to detailed structural analysis. By combining structural constraints from a series of experimental techniques spanning five orders of magnitude in length scale--including magic angle spinning nuclear magnetic resonance spectroscopy, X-ray fiber diffraction, cryoelectron microscopy, scanning transmission electron microscopy, and atomic force microscopy--we report the atomic-resolution (0.5 Å) structures of three amyloid polymorphs formed by an 11-residue peptide. These structures reveal the details of the packing interactions by which the constituent β-strands are assembled hierarchically into protofilaments, filaments, and mature fibrils.
History
DepositionFeb 27, 2013-
Header (metadata) releaseApr 3, 2013-
Map releaseApr 3, 2013-
UpdateNov 6, 2013-
Current statusNov 6, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 230.43
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 230.43
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-2m5k
  • Surface level: 230.43
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_5590.map.gz / Format: CCP4 / Size: 16 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of doublet cross-beta amyloid fibril polymorph
Voxel sizeX=Y=Z: 1.8 Å
Density
Contour LevelBy AUTHOR: 230.430000000000007 / Movie #1: 230.43
Minimum - Maximum-129.46867370999999 - 860.173217769999951
Average (Standard dev.)19.60117722 (±97.20013428)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-59-60-149
Dimensions120120298
Spacing120120298
CellA: 216.0 Å / B: 216.0 Å / C: 536.39996 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.81.81.8
M x/y/z120120298
origin x/y/z0.0000.0000.000
length x/y/z216.000216.000536.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-5029166
NX/NY/NZ106122134
MAP C/R/S123
start NC/NR/NS-60-59-149
NC/NR/NS120120298
D min/max/mean-129.469860.17319.601

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Supplemental data

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Sample components

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Entire : Doublet cross-beta amyloid fibril polymorph

EntireName: Doublet cross-beta amyloid fibril polymorph
Components
  • Sample: Doublet cross-beta amyloid fibril polymorph
  • Protein or peptide: Transthyretin(105-115)

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Supramolecule #1000: Doublet cross-beta amyloid fibril polymorph

SupramoleculeName: Doublet cross-beta amyloid fibril polymorph / type: sample / ID: 1000 / Number unique components: 1

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Macromolecule #1: Transthyretin(105-115)

MacromoleculeName: Transthyretin(105-115) / type: protein_or_peptide / ID: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Rattus norvegicus (Norway rat) / synonym: rat

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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

Concentration1 mg/mL
BufferpH: 2 / Details: 10% acetonitrile/water solution
GridDetails: holey carbon films (R2/2, QuantifoilMicro Tools GmbH, Jena, Germany)
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 99 K / Instrument: HOMEMADE PLUNGER
Method: Fibrils were applied to holey carbon films that were immediately plunge-frozen at liquid nitrogen temperature.

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 40000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 40000
Sample stageSpecimen holder: Nitrogen cooled / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureMin: 99 K / Max: 100 K / Average: 99 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification.
DateMar 3, 2006
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Number real images: 250
Tilt angle min0
Tilt angle max0
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: CTFFIND3
Final two d classificationNumber classes: 18
Final reconstructionApplied symmetry - Helical parameters - Δz: 4.67 Å
Applied symmetry - Helical parameters - Δ&Phi: 0.85 °
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.7 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER, IMAGIC, BKRP / Number images used: 82
DetailsThe particles were selected using an automatic selection program.

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