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- EMDB-4452: AL amyloid fibril from a lambda 1 light chain -

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Basic information

Entry
Database: EMDB / ID: EMD-4452
TitleAL amyloid fibril from a lambda 1 light chain
Map data
Sample
  • Complex: Amyloid fibril of an antibody lambda 1 light chain
    • Protein or peptide: lambda 1 light chain fragment, residues 3-118
Biological speciesHomo sapiens (human) / Human (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsRadamaker L / Schmidt M / Faendrich M / Fritz G
CitationJournal: Nat Commun / Year: 2019
Title: Cryo-EM structure of a light chain-derived amyloid fibril from a patient with systemic AL amyloidosis.
Authors: Lynn Radamaker / Yin-Hsi Lin / Karthikeyan Annamalai / Stefanie Huhn / Ute Hegenbart / Stefan O Schönland / Günter Fritz / Matthias Schmidt / Marcus Fändrich /
Abstract: Amyloid fibrils derived from antibody light chains are key pathogenic agents in systemic AL amyloidosis. They can be deposited in multiple organs but cardiac amyloid is the major risk factor of ...Amyloid fibrils derived from antibody light chains are key pathogenic agents in systemic AL amyloidosis. They can be deposited in multiple organs but cardiac amyloid is the major risk factor of mortality. Here we report the structure of a λ1 AL amyloid fibril from an explanted human heart at a resolution of 3.3 Å which we determined using cryo-electron microscopy. The fibril core consists of a 91-residue segment presenting an all-beta fold with ten mutagenic changes compared to the germ line. The conformation differs substantially from natively folded light chains: a rotational switch around the intramolecular disulphide bond being the crucial structural rearrangement underlying fibril formation. Our structure provides insight into the mechanism of protein misfolding and the role of patient-specific mutations in pathogenicity.
History
DepositionDec 2, 2018-
Header (metadata) releaseDec 19, 2018-
Map releaseApr 3, 2019-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.056
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.056
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ic3
  • Surface level: 0.056
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4452.png

Downloads & links

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Map

FileDownload / File: emd_4452.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 320 pix.
= 333.12 Å		1.04 Å/pix.
x 320 pix.
= 333.12 Å		1.04 Å/pix.
x 320 pix.
= 333.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.041 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.056 / Movie #1: 0.056
Minimum - Maximum-0.042287648 - 0.09975388
Average (Standard dev.)0.0001230849 (±0.0020280501)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 333.12 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0411.0411.041
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z333.120333.120333.120
α/β/γ90.00090.00090.000
start NX/NY/NZ-383-383-383
NX/NY/NZ768768768
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0420.1000.000

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Supplemental data

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Sample components

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Entire : Amyloid fibril of an antibody lambda 1 light chain

EntireName: Amyloid fibril of an antibody lambda 1 light chain
Components
  • Complex: Amyloid fibril of an antibody lambda 1 light chain
    • Protein or peptide: lambda 1 light chain fragment, residues 3-118

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Supramolecule #1: Amyloid fibril of an antibody lambda 1 light chain

SupramoleculeName: Amyloid fibril of an antibody lambda 1 light chain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Extracted fibrils from the heart of a patient suffering from systemic AL amyloidosis
Source (natural)Organism: Homo sapiens (human) / Organ: heart / Tissue: heart muscle
Molecular weightExperimental: 2.5 kDa/nm

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Macromolecule #1: lambda 1 light chain fragment, residues 3-118

MacromoleculeName: lambda 1 light chain fragment, residues 3-118 / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Human (human) / Organ: Heart / Tissue: heart muscle
Molecular weightTheoretical: 12.177463 KDa
SequenceString:
VLTQPPSASG TPGQRVTISC SGRSSNIGRN LVKWYQQFPG TAPKLLIYSN DQRPSGVPDR FSGSKSGTSA SLAVSGLQSE DEADYYCAA WDATLNAWVF GGGTKLTVLS QPKAAPS

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7 / Component - Formula: H2O / Component - Name: distilled water
GridModel: C-flat-1.2/1.3 4C / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 294 K / Instrument: GATAN CRYOPLUNGE 3
Details: blotted from the backside for 4 s before plunging.
DetailsSample in pure water, pH not determined

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-30 / Number grids imaged: 1 / Number real images: 847 / Average exposure time: 6.0 sec. / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
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

DetailsMotion-corrected and dose-weighted movie frames
Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 4.81 Å
Applied symmetry - Helical parameters - Δ&Phi: 0.58 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1.0) / Number images used: 32677
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Details: CTF was estimated from the non-dose-weighted micrographs
Segment selectionNumber selected: 119395
Details: manual selection. Sigma contrast 3, lowpass filter 20 A
Startup modelType of model: NONE
Details: Initial model generation in RELION, followed by generation of a "single-fibril model" from two picked fibrils with clearly visible cross-overs
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsRefinement strategy included global minimization and local grid search and ADP were refined. Secondary structure restraints and NCS were applied during refinement.
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 111.4
Target criteria: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Output model

PDB-6ic3:
AL amyloid fibril from a lambda 1 light chain

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