7ZKY | pdb_00007zky

Amyloid fibril from human systemic AA amyloidosis (vascular variant)

• PDB DOI: https://doi.org/10.2210/pdb7ZKY/pdb
• EM Map EMD-14771: EMDB EMDataResource

• Classification: PROTEIN FIBRIL
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2022-04-13 Released: 2022-12-07 
• Deposition Author(s): Banerjee, S., Schmidt, M., Faendrich, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.56 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: HELICAL 

Literature

Amyloid fibril structure from the vascular variant of systemic AA amyloidosis.

Banerjee, S., Baur, J., Daniel, C., Pfeiffer, P.B., Hitzenberger, M., Kuhn, L., Wiese, S., Bijzet, J., Haupt, C., Amann, K.U., Zacharias, M., Hazenberg, B.P.C., Westermark, G.T., Schmidt, M., Fandrich, M.

(2022) Nat Commun 13: 7261-7261

• PubMed: 36433936 
• DOI: https://doi.org/10.1038/s41467-022-34636-4
• Primary Citation Related Structures: 
  7ZKY


• PubMed Abstract: 
  

  Systemic AA amyloidosis is a debilitating protein misfolding disease in humans and animals. In humans, it occurs in two variants that are called 'vascular' and 'glomerular', depending on the main amyloid deposition site in the kidneys. Using cryo electron microscopy, we here show the amyloid fibril structure underlying the vascular disease variant. Fibrils purified from the tissue of such patients are mainly left-hand twisted and contain two non-equal stacks of fibril proteins. They contrast in these properties to the fibrils from the glomerular disease variant which are right-hand twisted and consist of two structurally equal stacks of fibril proteins. Our data demonstrate that the different disease variants in systemic AA amyloidosis are associated with different fibril morphologies.

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Organizational Affiliation: 
• Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany.
Department of Nephropathology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany.
Physics Department (T38), Technical University of Munich, 85748, Garching, Germany.
Core Unit Mass Spectrometry and Proteomics, Ulm University, 89081, Ulm, Germany.
Amyloidosis Center of Expertise, University Medical Center Groningen, University of Groningen, PO Box 30.001, 9700 RB, Groningen, The Netherlands.
Department of Medical Cell Biology, Uppsala University, SE-75123, Uppsala, Sweden.
Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 12-mer - A6B6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 93.31 kDa 
• Atom Count: 5,238 
• Modeled Residue Count: 642 
• Deposited Residue Count: 816 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amyloid protein A	A [auth B], B [auth A], C [auth D], D [auth C], E [auth F], F [auth E], G [auth H], H [auth G], I [auth J], J [auth I], K [auth L], L [auth K]	68	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P0DJI8 (Homo sapiens) Explore P0DJI8  Go to UniProtKB:  P0DJI8
PHAROS:  P0DJI8 GTEx:  ENSG00000173432

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.56 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: HELICAL 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-12-07 
Deposition Author(s): Banerjee, S., Schmidt, M., Faendrich, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-12-07
  Type: Initial release
  
• Version 1.1: 2024-07-24
  Changes: Data collection