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- EMDB-3994: Morphology X - cross-beta amyloid fibril structure from the IGSNV... -

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Basic information

Entry
Database: EMDB / ID: EMD-3994
TitleMorphology X - cross-beta amyloid fibril structure from the IGSNVVTWYQQL peptide of AL immunoglobulin light chain by cryo-EM
Map data
Sample
  • Complex: Amyloidogenic Fragment IGSNVVTWYQQL of Immunoglobulin Light Chain of a Human AL Patient
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 17.7 Å
AuthorsClose W / Faendrich M
CitationJournal: Nat Commun / Year: 2018
Title: Physical basis of amyloid fibril polymorphism.
Authors: William Close / Matthias Neumann / Andreas Schmidt / Manuel Hora / Karthikeyan Annamalai / Matthias Schmidt / Bernd Reif / Volker Schmidt / Nikolaus Grigorieff / Marcus Fändrich /
Abstract: Polymorphism is a key feature of amyloid fibril structures but it remains challenging to explain these variations for a particular sample. Here, we report electron cryomicroscopy-based ...Polymorphism is a key feature of amyloid fibril structures but it remains challenging to explain these variations for a particular sample. Here, we report electron cryomicroscopy-based reconstructions from different fibril morphologies formed by a peptide fragment from an amyloidogenic immunoglobulin light chain. The observed fibril morphologies vary in the number and cross-sectional arrangement of a structurally conserved building block. A comparison with the theoretically possible constellations reveals the experimentally observed spectrum of fibril morphologies to be governed by opposing sets of forces that primarily arise from the β-sheet twist, as well as peptide-peptide interactions within the fibril cross-section. Our results provide a framework for rationalizing and predicting the structure and polymorphism of cross-β fibrils, and suggest that a small number of physical parameters control the observed fibril architectures.
History
DepositionNov 15, 2017-
Header (metadata) releaseDec 20, 2017-
Map releaseFeb 28, 2018-
UpdateFeb 28, 2018-
Current statusFeb 28, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 138
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 138
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3994.png

Downloads & links

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Map

FileDownload / File: emd_3994.map.gz / Format: CCP4 / Size: 84.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 1540 pix.
= 1617. Å		1.05 Å/pix.
x 120 pix.
= 126. Å		1.05 Å/pix.
x 120 pix.
= 126. 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: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 138. / Movie #1: 138
Minimum - Maximum-269.373899999999992 - 529.882100000000037
Average (Standard dev.)32.513793999999997 (±128.756329999999991)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin484819
Dimensions1201201540
Spacing1201201540
CellA: 125.99999 Å / B: 125.99999 Å / C: 1616.9999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z1201201540
origin x/y/z0.0000.0000.000
length x/y/z126.000126.0001617.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS484819
NC/NR/NS1201201540
D min/max/mean-269.374529.88232.514

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Supplemental data

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Sample components

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Entire : Amyloidogenic Fragment IGSNVVTWYQQL of Immunoglobulin Light Chain...

EntireName: Amyloidogenic Fragment IGSNVVTWYQQL of Immunoglobulin Light Chain of a Human AL Patient
Components
  • Complex: Amyloidogenic Fragment IGSNVVTWYQQL of Immunoglobulin Light Chain of a Human AL Patient

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Supramolecule #1: Amyloidogenic Fragment IGSNVVTWYQQL of Immunoglobulin Light Chain...

SupramoleculeName: Amyloidogenic Fragment IGSNVVTWYQQL of Immunoglobulin Light Chain of a Human AL Patient
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: synthetic construct (others)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration5.00 mg/mL
BufferpH: 8 / Component - Concentration: 50.0 mM / Component - Name: Tris
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 50 % / Instrument: GATAN CRYOPLUNGE 3
Details: Incubation of fibril solution on glow discharged holey carbon grid for 30 seconds and backside blotting for 4 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7420 pixel / Digitization - Dimensions - Height: 7676 pixel / Digitization - Frames/image: 1-73 / Number real images: 458 / Average exposure time: 21.9 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.69 Å
Applied symmetry - Helical parameters - Δ&Phi: 0.72 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 17.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIX (ver. 1.1) / Number images used: 374
CTF correctionSoftware - Name: CTFFIND (ver. 4.0.4)
Startup modelType of model: NONE / Details: Startup model was generated using FREALIX
Final angle assignmentType: NOT APPLICABLE / Software - Name: FREALIX (ver. 1.1)
FSC plot (resolution estimation)

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