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- EMDB-2323: Electron cryo-microscopy of a cross-beta amyloid fibril polymorph -

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Basic information

Entry
Database: EMDB / ID: EMD-2323
TitleElectron cryo-microscopy of a cross-beta amyloid fibril polymorph
Map dataReconstruction of triplet cross-beta amyloid fibril polymorph
Sample
  • Sample: Triplet 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 / thyroid hormone binding / Neutrophil degranulation / negative regulation of glomerular filtration / small molecule binding / hormone binding / purine nucleobase metabolic process / molecular sequestering activity ...The canonical retinoid cycle in rods (twilight vision) / Retinoid metabolism and transport / thyroid hormone metabolic process / thyroid hormone binding / Neutrophil degranulation / negative regulation of glomerular filtration / small molecule binding / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / phototransduction, visible light / retinoid metabolic process / hormone activity / protein-containing complex binding / protein-containing complex / extracellular space / 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 speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.2 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.NAT.ACAD.SCI.USA / Year: 2013
Title: Atomic structure and hierarchical assembly of a cross-beta amyloid fibril
Authors: Fitzpatrick AW / Debelouchina GT / Bayro MJ / Clare DK / Caporini MA / Bajaj VS / Jaroniec CP / Wang L / Ladizhansky V / Muller SA / Macphee CE / Waudby CA / Mott HR / De Simone A / Knowles ...Authors: Fitzpatrick AW / Debelouchina GT / Bayro MJ / Clare DK / Caporini MA / Bajaj VS / Jaroniec CP / Wang L / Ladizhansky V / Muller SA / Macphee CE / Waudby CA / Mott HR / De Simone A / Knowles TP / Saibil HR / Vendruscolo M / Orlova EV / Griffin RG / Dobson CM
History
DepositionFeb 27, 2013-
Header (metadata) releaseMar 27, 2013-
Map releaseMar 27, 2013-
UpdateDec 18, 2013-
Current statusDec 18, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 299.5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 299.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-2m5m
  • Surface level: 299.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-2m5m
  • Surface level: 299.5
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2m5m
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

2323.tif

Downloads & links

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Map

FileDownload / File: emd_2323.map.gz / Format: CCP4 / Size: 16 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of triplet cross-beta amyloid fibril polymorph
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.8 Å/pix.
x 298 pix.
= 536.4 Å		1.8 Å/pix.
x 120 pix.
= 216. Å		1.8 Å/pix.
x 120 pix.
= 216. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 299.5 / Movie #1: 299.5
Minimum - Maximum-187.412612919999987 - 863.487976069999945
Average (Standard dev.)32.261600489999999 (±122.427833559999996)
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-36-12-40
NX/NY/NZ732581
MAP C/R/S123
start NC/NR/NS-60-59-149
NC/NR/NS120120298
D min/max/mean-187.413863.48832.262

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Supplemental data

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Sample components

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Entire : Triplet cross-beta amyloid fibril polymorph

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

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Supramolecule #1000: Triplet cross-beta amyloid fibril polymorph

SupramoleculeName: Triplet 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 / Name.synonym: TTR(105-115) / Recombinant expression: No
Source (natural)Organism: Rattus norvegicus (Norway rat) / synonym: Norway Rat
SequenceUniProtKB: Transthyretin

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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: For cryo-EM imaging, fibrils were applied to holey carbon films (R2/2, QuantifoilMicro Tools GmbH, Jena, Germany) that were immediately plunge-frozen at liquid nitrogen temperature.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 99 K / Instrument: HOMEMADE PLUNGER
Method: For cryo-EM imaging, fibrils were applied to holey carbon films (R2/2, QuantifoilMicro Tools GmbH, Jena, Germany) that were immediately plunge-frozen at liquid nitrogen temperature.

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Electron microscopy

MicroscopeFEI TECNAI F20
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
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 40000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsThe particles were selected using an automatic selection program.
CTF correctionDetails: CTFFIND3
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.2 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIER, IMAGIC, BKRP / Number images used: 152
Final two d classificationNumber classes: 28

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