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- EMDB-3128: Structure of a cross-beta amyloid fibril from IGSNVVTWYQQL peptid... -

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Basic information

Entry
Database: EMDB / ID: EMD-3128
TitleStructure of a cross-beta amyloid fibril from IGSNVVTWYQQL peptide of AL-DIA immunoglobulin light chain by cryo-EM and fiber diffraction
Map dataReconstruction morphology 1 of a left-handed amyloid-like fibril of the IGSNVVTWYQQL fragment of an immunoglobulin light chain
Sample
  • Sample: Amyloidogenic Fragment IGSNVVTWYQQL of Immunoglobulin Light Chain of Human AL Patient
  • Protein or peptide: Immunoglobulin Light Chain
KeywordsAL amyloidosis / cryo electron microscopy / steric zipper / three dimensional reconstruction
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 8.3 Å
AuthorsSchmidt A / Annamalai K / Schmidt M / Grigorieff N / Fandrich M
CitationJournal: Proc Natl Acad Sci U S A / Year: 2016
Title: Cryo-EM reveals the steric zipper structure of a light chain-derived amyloid fibril.
Authors: Andreas Schmidt / Karthikeyan Annamalai / Matthias Schmidt / Nikolaus Grigorieff / Marcus Fändrich /
Abstract: Amyloid fibrils are proteinaceous aggregates associated with diseases in humans and animals. The fibrils are defined by intermolecular interactions between the fibril-forming polypeptide chains, but ...Amyloid fibrils are proteinaceous aggregates associated with diseases in humans and animals. The fibrils are defined by intermolecular interactions between the fibril-forming polypeptide chains, but it has so far remained difficult to reveal the assembly of the peptide subunits in a full-scale fibril. Using electron cryomicroscopy (cryo-EM), we present a reconstruction of a fibril formed from the pathogenic core of an amyloidogenic immunoglobulin (Ig) light chain. The fibril density shows a lattice-like assembly of face-to-face packed peptide dimers that corresponds to the structure of steric zippers in peptide crystals. Interpretation of the density map with a molecular model enabled us to identify the intermolecular interactions between the peptides and rationalize the hierarchical structure of the fibril based on simple chemical principles.
History
DepositionAug 13, 2015-
Header (metadata) releaseSep 16, 2015-
Map releaseMay 18, 2016-
UpdateJun 15, 2016-
Current statusJun 15, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.85
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.85
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3128.png

Downloads & links

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Map

FileDownload / File: emd_3128.map.gz / Format: CCP4 / Size: 2.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction morphology 1 of a left-handed amyloid-like fibril of the IGSNVVTWYQQL fragment of an immunoglobulin light chain
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.11 Å/pix.
x 160 pix.
= 337.6 Å		2.11 Å/pix.
x 70 pix.
= 147.7 Å		2.11 Å/pix.
x 70 pix.
= 147.7 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: 2.11 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.85 / Movie #1: 0.85
Minimum - Maximum-1968.878540039999962 - 8991.770507810000709
Average (Standard dev.)1234.688354489999938 (±2857.944335940000201)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-35-35-80
Dimensions7070160
Spacing7070160
CellA: 147.7 Å / B: 147.7 Å / C: 337.59998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.112.112.11
M x/y/z7070160
origin x/y/z0.0000.0000.000
length x/y/z147.700147.700337.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-35-35-80
NC/NR/NS7070160
D min/max/mean-1968.8798991.7711234.688

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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 Human AL Patient
Components
  • Sample: Amyloidogenic Fragment IGSNVVTWYQQL of Immunoglobulin Light Chain of Human AL Patient
  • Protein or peptide: Immunoglobulin Light Chain

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Supramolecule #1000: Amyloidogenic Fragment IGSNVVTWYQQL of Immunoglobulin Light Chain...

SupramoleculeName: Amyloidogenic Fragment IGSNVVTWYQQL of Immunoglobulin Light Chain of Human AL Patient
type: sample / ID: 1000 / Details: The sample forms long amyloid-like fibrils. / Number unique components: 1

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Macromolecule #1: Immunoglobulin Light Chain

MacromoleculeName: Immunoglobulin Light Chain / type: protein_or_peptide / ID: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Blood / Cell: Plasma Cell / Location in cell: extracellular

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration5.0 mg/mL
BufferpH: 8 / Details: 50mM Tris-HCL
GridDetails: C-flat 1.2/1.3-2C 400 mesh grids, glow discharged
VitrificationCryogen name: ETHANE / Chamber humidity: 50 % / Chamber temperature: 100 K / Instrument: GATAN CRYOPLUNGE 3
Method: Incubation of 0.014 mg/ml 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 TECNAI F20
TemperatureAverage: 100 K
DateNov 12, 2012
Image recordingCategory: CCD / Film or detector model: FEI FALCON I (4k x 4k) / Number real images: 10 / Average electron dose: 25 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 66350.7 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / 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: 1.464 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.3 Å / Resolution method: OTHER / Software - Name: Frealix
Details: Final map was calculated from eleven single fibril reconstructions.
CTF correctionDetails: Defocus estimated for each helical subunit
FSC plot (resolution estimation)

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