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- EMDB-12570: AL amyloid fibril from a lambda 1 light chain -

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Basic information

Entry
Database: EMDB / ID: EMD-12570
TitleAL amyloid fibril from a lambda 1 light chain
Map data
SampleAmyloid fibril of an antibody lambda 1 immunoglobulin light chain:
Amyloid lambda1 light chain
Biological speciesHomo sapiens (human) / Human (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsKarimi Farsijani S / Radamaker L / Fandrich M
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR2969 Germany
CitationJournal: Nat Commun / Year: 2021
Title: Role of mutations and post-translational modifications in systemic AL amyloidosis studied by cryo-EM.
Authors: Lynn Radamaker / Sara Karimi-Farsijani / Giada Andreotti / Julian Baur / Matthias Neumann / Sarah Schreiner / Natalie Berghaus / Raoul Motika / Christian Haupt / Paul Walther / Volker ...Authors: Lynn Radamaker / Sara Karimi-Farsijani / Giada Andreotti / Julian Baur / Matthias Neumann / Sarah Schreiner / Natalie Berghaus / Raoul Motika / Christian Haupt / Paul Walther / Volker Schmidt / Stefanie Huhn / Ute Hegenbart / Stefan O Schönland / Sebastian Wiese / Clarissa Read / Matthias Schmidt / Marcus Fändrich /
Abstract: Systemic AL amyloidosis is a rare disease that is caused by the misfolding of immunoglobulin light chains (LCs). Potential drivers of amyloid formation in this disease are post-translational ...Systemic AL amyloidosis is a rare disease that is caused by the misfolding of immunoglobulin light chains (LCs). Potential drivers of amyloid formation in this disease are post-translational modifications (PTMs) and the mutational changes that are inserted into the LCs by somatic hypermutation. Here we present the cryo electron microscopy (cryo-EM) structure of an ex vivo λ1-AL amyloid fibril whose deposits disrupt the ordered cardiomyocyte structure in the heart. The fibril protein contains six mutational changes compared to the germ line and three PTMs (disulfide bond, N-glycosylation and pyroglutamylation). Our data imply that the disulfide bond, glycosylation and mutational changes contribute to determining the fibril protein fold and help to generate a fibril morphology that is able to withstand proteolytic degradation inside the body.
History
DepositionMar 8, 2021-
Header (metadata) releaseNov 24, 2021-
Map releaseNov 24, 2021-
UpdateNov 24, 2021-
Current statusNov 24, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 12
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 12
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7nsl
  • Surface level: 12
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7nsl
  • Imaged by Jmol
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12570.png

Downloads & links

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Map

FileDownload / File: emd_12570.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesX (Sec.)Y (Row.)Z (Col.)
1.04 Å/pix.
x 260 pix.
= 270.4 Å		1.04 Å/pix.
x 260 pix.
= 270.4 Å		1.04 Å/pix.
x 260 pix.
= 270.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 12.0 / Movie #1: 12
Minimum - Maximum-24.973225 - 49.14803
Average (Standard dev.)-1.8761297e-12 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 270.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z260260260
origin x/y/z0.0000.0000.000
length x/y/z270.400270.400270.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ260260260
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS260260260
D min/max/mean-24.97349.148-0.000

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Supplemental data

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Half map: #2

Fileemd_12570_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_12570_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 Amyloid fibril of an antibody lambda 1 immunoglobulin light chain

EntireName: Amyloid fibril of an antibody lambda 1 immunoglobulin light chain
Details: Extracted fibrils from the explanted heart of a patient suffering from systemic AL amyloidosis
Number of Components: 2

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Component #1: protein, Amyloid fibril of an antibody lambda 1 immunoglobulin li...

ProteinName: Amyloid fibril of an antibody lambda 1 immunoglobulin light chain
Details: Extracted fibrils from the explanted heart of a patient suffering from systemic AL amyloidosis
Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (natural)Organ Or Tissue: Heart

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Component #2: protein, Amyloid lambda1 light chain

ProteinName: Amyloid lambda1 light chain / Number of Copies: 7 / Recombinant expression: No
MassTheoretical: 12.122354 kDa
SourceSpecies: Human (human)
Source (natural)Organ Or Tissue: Heart

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Experimental details

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Sample preparation

SpecimenSpecimen State: Filament / Method: cryo EM
Helical ParametersAxial Symmetry: C1 (asymmetric) / Delta Z: 4.76311 Å / Delta Phi: -1.45566 %deg;
Sample solutionpH: 7
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen Name: ETHANE / Temperature: 295 K / Humidity: 95 % / Details: blot for 9s before plunging.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 40 e/Å2 / Illumination Mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging Mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of Digital Images: 3032

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Image processing

ProcessingMethod: helical reconstruction / Details: Motion-corrected and dose-weighted movie frames
3D reconstructionSoftware: RELION
CTF correction: CTF was estimated from the non-dose-weighted micrographs
Resolution: 3.1 Å / Resolution Method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Target Criteria: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refinement space: REAL
Details: Secondary structure restraints and NCS were applied during refinement
Output model

7nsl

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