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- EMDB-51031: Cryo-electron tomogram of AL59 amyloids interacting with collagen VI -

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Entry
Database: EMDB / ID: EMD-51031
TitleCryo-electron tomogram of AL59 amyloids interacting with collagen VI
Map dataTomogram of Figure 1B, middle panel showing a collagen VI fibril. Figure shows slice 108.
Sample
  • Complex: Sample extracted from a patient of Light Chain Amyloidosis
KeywordsAL59 / Collagen IV / Amyloid / Protein Interaction / Light Chain Amyloidosis / PROTEIN BINDING
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM
AuthorsSicking K / Fernandez-Busnadiego R / Ricagno S
Funding support Germany, United States, Italy, 4 items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC 2067/1-390729940 Germany
German Research Foundation (DFG)448415290 Germany
Michael J. Fox FoundationASAP-000282 United States
Fondazione CARIPLOGJC23044 Italy
Citation
Journal: Nat Commun / Year: 2024
Title: Helical superstructures between amyloid and collagen in cardiac fibrils from a patient with AL amyloidosis.
Authors: Tim Schulte / Antonio Chaves-Sanjuan / Valentina Speranzini / Kevin Sicking / Melissa Milazzo / Giulia Mazzini / Paola Rognoni / Serena Caminito / Paolo Milani / Chiara Marabelli / ...Authors: Tim Schulte / Antonio Chaves-Sanjuan / Valentina Speranzini / Kevin Sicking / Melissa Milazzo / Giulia Mazzini / Paola Rognoni / Serena Caminito / Paolo Milani / Chiara Marabelli / Alessandro Corbelli / Luisa Diomede / Fabio Fiordaliso / Luigi Anastasia / Carlo Pappone / Giampaolo Merlini / Martino Bolognesi / Mario Nuvolone / Rubén Fernández-Busnadiego / Giovanni Palladini / Stefano Ricagno /
Abstract: Systemic light chain (LC) amyloidosis (AL) is a disease where organs are damaged by an overload of a misfolded patient-specific antibody-derived LC, secreted by an abnormal B cell clone. The high LC ...Systemic light chain (LC) amyloidosis (AL) is a disease where organs are damaged by an overload of a misfolded patient-specific antibody-derived LC, secreted by an abnormal B cell clone. The high LC concentration in the blood leads to amyloid deposition at organ sites. Indeed, cryogenic electron microscopy (cryo-EM) has revealed unique amyloid folds for heart-derived fibrils taken from different patients. Here, we present the cryo-EM structure of heart-derived AL amyloid (AL59) from another patient with severe cardiac involvement. The double-layered structure displays a u-shaped core that is closed by a β-arc lid and extended by a straight tail. Noteworthy, the fibril harbours an extended constant domain fragment, thus ruling out the variable domain as sole amyloid building block. Surprisingly, the fibrils were abundantly concatenated with a proteinaceous polymer, here identified as collagen VI (COLVI) by immuno-electron microscopy (IEM) and mass-spectrometry. Cryogenic electron tomography (cryo-ET) showed how COLVI wraps around the amyloid forming a helical superstructure, likely stabilizing and protecting the fibrils from clearance. Thus, here we report structural evidence of interactions between amyloid and collagen, potentially signifying a distinct pathophysiological mechanism of amyloid deposits.
#1: Journal: Res Sq / Year: 2023
Title: Helical superstructures between amyloid and collagen VI in heart-derived fibrils from a patient with Light Chain Amyloidosis.
Authors: Ricagno S / Schulte T / Chaves-Sanjuan A / Speranzini V / Sicking K / Mazzini G / Rognoni P / Caminito S / Milani P / Marabelli C / Corbelli A / Diomede L / Fiordaliso F / Anastasia L / ...Authors: Ricagno S / Schulte T / Chaves-Sanjuan A / Speranzini V / Sicking K / Mazzini G / Rognoni P / Caminito S / Milani P / Marabelli C / Corbelli A / Diomede L / Fiordaliso F / Anastasia L / Pappone C / merlini G / Bolognesi M / Nuvolone M / Fernandez-Busnadiego R / Palladini G
History
DepositionJul 15, 2024-
Header (metadata) releaseAug 7, 2024-
Map releaseAug 7, 2024-
UpdateAug 7, 2024-
Current statusAug 7, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51031.png

Downloads & links

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Map

FileDownload / File: emd_51031.map.gz / Format: CCP4 / Size: 800 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTomogram of Figure 1B, middle panel showing a collagen VI fibril. Figure shows slice 108.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
9.25 Å/pix.
x 1024 pix.
= 9472. Å		9.25 Å/pix.
x 200 pix.
= 1850. Å		9.25 Å/pix.
x 1024 pix.
= 9472. Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 9.25 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-4916.9399999999996 - 4074.462599999999838
Average (Standard dev.)59.899943999999998 (±175.298750000000013)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-10000
Dimensions20010241024
Spacing10242001024
CellA: 9472.0 Å / B: 1850.0 Å / C: 9472.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Sample extracted from a patient of Light Chain Amyloidosis

EntireName: Sample extracted from a patient of Light Chain Amyloidosis
Components
  • Complex: Sample extracted from a patient of Light Chain Amyloidosis

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Supramolecule #1: Sample extracted from a patient of Light Chain Amyloidosis

SupramoleculeName: Sample extracted from a patient of Light Chain Amyloidosis
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human) / Tissue: Heart

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statefilament

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Sample preparation

BufferpH: 7 / Details: water
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Details: 30mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.0 K / Instrument: FEI VITROBOT MARK IV
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Electron Microscopy Sciences / Diameter: 10 nm

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 120.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 53000
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

Final reconstructionSoftware - Name: IMOD (ver. 4.11.15) / Number images used: 35

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