9FAA | pdb_00009faa

Cryo-EM structure of cardiac collagen-associated amyloid AL59


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation 3D Report Full Report

Validation slider image for 9FAA

This is version 1.3 of the entry. See complete history

Literature

Helical superstructures between amyloid and collagen in cardiac fibrils from a patient with AL amyloidosis.

Schulte, T.Chaves-Sanjuan, A.Speranzini, V.Sicking, K.Milazzo, M.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.Ricagno, S.

(2024) Nat Commun 15: 6359-6359

  • DOI: https://doi.org/10.1038/s41467-024-50686-2
  • Primary Citation Related Structures: 
    9FAA, 9FAC

  • PubMed 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 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.


  • Organizational Affiliation
    • Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, Piazza Malan 2, 20097, San Donato Milanese, Italy.

Macromolecule Content 

  • Total Structure Weight: 70.72 kDa 
  • Atom Count: 4,460 
  • Modeled Residue Count: 590 
  • Deposited Residue Count: 660 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Monoclonal immunoglobulin light chains (LC)A,
B [auth D],
C,
D [auth B],
E
132Homo sapiensMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Italian Ministry of EducationItalyPRIN 2020 (20207XLJB2)

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-17
    Type: Initial release
  • Version 1.1: 2024-08-14
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Structure summary
  • Version 1.3: 2025-07-09
    Changes: Data collection