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- EMDB-0274: Cryo-EM structure of cardiac amyloid fibrils from an immunoglobul... -

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Entry
Database: EMDB / ID: EMD-0274
TitleCryo-EM structure of cardiac amyloid fibrils from an immunoglobulin light chain (AL) amyloidosis patient.
Map data3D helical reconstrutcion of an amyloid fibrils from an immunoglobulin light chain (AL) amyloidosis patient.
Sample
  • Complex: Cardiac amyloid fibril from an immunoglobulin light chain (AL) amyloidosis patient
    • Protein or peptide: Monoclonal immunoglobulin light chains (LC)
Keywordsimmunoglobulin light chains / amyloid cardiomyopathy / ex-vivo cryo-EM / helical reconstruction / PROTEIN FIBRIL
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsSwuec P
Funding support Italy, 4 items
OrganizationGrant numberCountry
Italian Association for Cancer Research9965 Italy
Fondazione CARIPLO
Italian Ministry of Health
Italian Medicines Agency
CitationJournal: Nat Commun / Year: 2019
Title: Cryo-EM structure of cardiac amyloid fibrils from an immunoglobulin light chain AL amyloidosis patient.
Authors: Paolo Swuec / Francesca Lavatelli / Masayoshi Tasaki / Cristina Paissoni / Paola Rognoni / Martina Maritan / Francesca Brambilla / Paolo Milani / Pierluigi Mauri / Carlo Camilloni / Giovanni ...Authors: Paolo Swuec / Francesca Lavatelli / Masayoshi Tasaki / Cristina Paissoni / Paola Rognoni / Martina Maritan / Francesca Brambilla / Paolo Milani / Pierluigi Mauri / Carlo Camilloni / Giovanni Palladini / Giampaolo Merlini / Stefano Ricagno / Martino Bolognesi /
Abstract: Systemic light chain amyloidosis (AL)  is a life-threatening disease caused by aggregation and deposition of monoclonal immunoglobulin light chains (LC) in target organs. Severity of heart ...Systemic light chain amyloidosis (AL)  is a life-threatening disease caused by aggregation and deposition of monoclonal immunoglobulin light chains (LC) in target organs. Severity of heart involvement is the most important factor determining prognosis. Here, we report the 4.0 Å resolution cryo-electron microscopy map and molecular model of amyloid fibrils extracted from the heart of an AL amyloidosis patient with severe amyloid cardiomyopathy. The helical fibrils are composed of a single protofilament, showing typical 4.9 Å stacking and cross-β architecture. Two distinct polypeptide stretches (total of 77 residues) from the LC variable domain (V) fit the fibril density. Despite V high sequence variability, residues stabilizing the fibril core are conserved through different cardiotoxic V, highlighting structural motifs that may be common to misfolding-prone LCs. Our data shed light on the architecture of LC amyloids, correlate amino acid sequences with fibril assembly, providing the grounds for development of innovative medicines.
History
DepositionOct 6, 2018-
Header (metadata) releaseMar 27, 2019-
Map releaseMar 27, 2019-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0375
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0375
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6hud
  • Surface level: 0.0375
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0274.png

Downloads & links

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Map

FileDownload / File: emd_0274.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D helical reconstrutcion of an amyloid fibrils from an immunoglobulin light chain (AL) amyloidosis patient.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 320 pix.
= 283.84 Å		0.89 Å/pix.
x 320 pix.
= 283.84 Å		0.89 Å/pix.
x 320 pix.
= 283.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.887 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0375 / Movie #1: 0.0375
Minimum - Maximum-0.07641551 - 0.1258171
Average (Standard dev.)0.0001584446 (±0.002512264)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 283.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8870.8870.887
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z283.840283.840283.840
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-0.0760.1260.000

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Supplemental data

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Sample components

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Entire : Cardiac amyloid fibril from an immunoglobulin light chain (AL) am...

EntireName: Cardiac amyloid fibril from an immunoglobulin light chain (AL) amyloidosis patient
Components
  • Complex: Cardiac amyloid fibril from an immunoglobulin light chain (AL) amyloidosis patient
    • Protein or peptide: Monoclonal immunoglobulin light chains (LC)

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Supramolecule #1: Cardiac amyloid fibril from an immunoglobulin light chain (AL) am...

SupramoleculeName: Cardiac amyloid fibril from an immunoglobulin light chain (AL) amyloidosis patient
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human) / Tissue: Heart

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Macromolecule #1: Monoclonal immunoglobulin light chains (LC)

MacromoleculeName: Monoclonal immunoglobulin light chains (LC) / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Tissue: Heart
Molecular weightTheoretical: 14.620864 KDa
SequenceString:
NFMLTQPHSV SESPGKTLTI SCTGSSASIA SHYVQWYQQR PGGAPTTLIY ENDQRPSEVP DRFSGSIDSS SNSASLTISG LKTEDEADY YCQSYDGNNH WVFGGGTKLT VLSQPKAAPS VTLFPPSSEE LQANKAT

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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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.01 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number real images: 1680 / Average exposure time: 1.0 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 120000
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.903 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.608 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1beta1) / Number images used: 21031
Segment selectionNumber selected: 104689 / Software - Name: RELION (ver. 2.1beta1)
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. v2.1beta1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-6hud:
Cryo-EM structure of cardiac amyloid fibrils from an immunoglobulin light chain (AL) amyloidosis patient.

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