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- EMDB-11031: AL amyloid fibril from a lambda 3 light chain in conformation A -

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Basic information

Entry
Database: EMDB / ID: EMD-11031
TitleAL amyloid fibril from a lambda 3 light chain in conformation A
Map data
SampleAmyloid fibril of an antibody lambda 3 immunoglobulin light chain
  • lambda 3 immunoglobulin light chain fragment, residues 2-116
Biological speciesHomo sapiens (human) / Human (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsRadamaker L / Fandrich M
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR2969 Germany
CitationJournal: Nat Commun / Year: 2021
Title: Cryo-EM reveals structural breaks in a patient-derived amyloid fibril from systemic AL amyloidosis.
Authors: Lynn Radamaker / Julian Baur / Stefanie Huhn / Christian Haupt / Ute Hegenbart / Stefan Schönland / Akanksha Bansal / Matthias Schmidt / Marcus Fändrich /
Abstract: Systemic AL amyloidosis is a debilitating and potentially fatal disease that arises from the misfolding and fibrillation of immunoglobulin light chains (LCs). The disease is patient-specific with ...Systemic AL amyloidosis is a debilitating and potentially fatal disease that arises from the misfolding and fibrillation of immunoglobulin light chains (LCs). The disease is patient-specific with essentially each patient possessing a unique LC sequence. In this study, we present two ex vivo fibril structures of a λ3 LC. The fibrils were extracted from the explanted heart of a patient (FOR005) and consist of 115-residue fibril proteins, mainly from the LC variable domain. The fibril structures imply that a 180° rotation around the disulfide bond and a major unfolding step are necessary for fibrils to form. The two fibril structures show highly similar fibril protein folds, differing in only a 12-residue segment. Remarkably, the two structures do not represent separate fibril morphologies, as they can co-exist at different z-axial positions within the same fibril. Our data imply the presence of structural breaks at the interface of the two structural forms.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionMay 14, 2020-
Header (metadata) releaseFeb 24, 2021-
Map releaseFeb 24, 2021-
UpdateFeb 24, 2021-
Current statusFeb 24, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 8
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 8
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6z1o
  • Surface level: 8
  • 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_11031.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.04 Å/pix.
x 300 pix.
= 312. Å
1.04 Å/pix.
x 300 pix.
= 312. Å
1.04 Å/pix.
x 300 pix.
= 312. 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
Contour LevelBy AUTHOR: 8.0 / Movie #1: 8
Minimum - Maximum-34.031025 - 62.29229
Average (Standard dev.)-8.499955e-12 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z312.000312.000312.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-34.03162.292-0.000

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Supplemental data

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Half map: #1

Fileemd_11031_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_11031_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Amyloid fibril of an antibody lambda 3 immunoglobulin light chain

EntireName: Amyloid fibril of an antibody lambda 3 immunoglobulin light chain
Details: Extracted fibrils from the explanted heart of a systemic AL amyloidosis patient
Number of components: 2

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Component #1: protein, Amyloid fibril of an antibody lambda 3 immunoglobulin li...

ProteinName: Amyloid fibril of an antibody lambda 3 immunoglobulin light chain
Details: Extracted fibrils from the explanted heart of a systemic AL amyloidosis patient
Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (natural)Organ or tissue: Heart

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Component #2: protein, lambda 3 immunoglobulin light chain fragment, residues 2-116

ProteinName: lambda 3 immunoglobulin light chain fragment, residues 2-116
Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 9.431303 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: 4.8 Å / Delta phi: -1.1 %deg;
Sample solutionpH: 7
Support film40 mA
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: 1964

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Image processing

ProcessingMethod: helical reconstruction / Details: Motion-corrected and dose-weighted movie frames
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION
CTF correction: CTF was estimated from the non-dose-weighted micrographs
Resolution: 3.2 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
Overall bvalue: 73.24
Output model

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