7NSL | pdb_00007nsl

AL amyloid fibril from a lambda 1 light chain

• PDB DOI: https://doi.org/10.2210/pdb7NSL/pdb
• EM Map EMD-12570: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2021-03-08 Released: 2021-11-24 
• Deposition Author(s): Karimi Farsijani, S., Radamaker, L., Fandrich, M.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Literature

Role of mutations and post-translational modifications in systemic AL amyloidosis studied by cryo-EM.

Radamaker, L., Karimi-Farsijani, S., Andreotti, G., Baur, J., Neumann, M., Schreiner, S., Berghaus, N., Motika, R., Haupt, C., Walther, P., Schmidt, V., Huhn, S., Hegenbart, U., Schonland, S.O., Wiese, S., Read, C., Schmidt, M., Fandrich, M.

(2021) Nat Commun 12: 6434-6434

• PubMed: 34741031 
• DOI: https://doi.org/10.1038/s41467-021-26553-9
• Primary Citation Related Structures: 
  7NSL


• PubMed Abstract: 
  

  Systemic AL amyloidosis is a rare disease that is caused by the misfolding of immunoglobulin light chains (LCs). Potential drivers of amyloid formation in this disease are post-translational modifications (PTMs) and the mutational changes that are inserted into the LCs by somatic hypermutation. Here we present the cryo electron microscopy (cryo-EM) structure of an ex vivo λ1-AL amyloid fibril whose deposits disrupt the ordered cardiomyocyte structure in the heart. The fibril protein contains six mutational changes compared to the germ line and three PTMs (disulfide bond, N-glycosylation and pyroglutamylation). Our data imply that the disulfide bond, glycosylation and mutational changes contribute to determining the fibril protein fold and help to generate a fibril morphology that is able to withstand proteolytic degradation inside the body.

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Organizational Affiliation: 
• Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany.
Institute of Stochastics, Ulm University, 89081, Ulm, Germany.
Medical Department V, Section of Multiple Myeloma, Heidelberg University Hospital, 69120, Heidelberg, Germany.
Department of Asia-Africa-Studies, Middle Eastern History and Culture, University of Hamburg, 20148, Hamburg, Germany.
Central Facility for Electron Microscopy, Ulm University, 89081, Ulm, Germany.
Medical Department V, Amyloidosis Center, Heidelberg University Hospital, 69120, Heidelberg, Germany.
Core Unit Mass Spectrometry and Proteomics, Medical Faculty, Ulm University, 89081, Ulm, Germany.
Institute of Virology, Ulm University Medical Center, 89081, Ulm, Germany.
Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 7-mer - A7 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 84.86 kDa 
• Atom Count: 4,270 
• Modeled Residue Count: 595 
• Deposited Residue Count: 826 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amyloid lambda1 light chain	A [auth D], B [auth E], C [auth F], D [auth C], E [auth B], F [auth A], G	118	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0
MODEL REFINEMENT	PHENIX	1.16

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-11-24 
Deposition Author(s): Karimi Farsijani, S., Radamaker, L., Fandrich, M.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	FOR2969

Revision History  

• Version 1.0: 2021-11-24
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Structure summary