Biological Assembly 1  

 3D View: Structure

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 18-mer - A18 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 81.36 kDa 
• Atom Count: 4230 
• Modelled Residue Count: 576 
• Deposited Residue Count: 756 
• Unique protein chains: 1

5KK3

Atomic Resolution Structure of Monomorphic AB42 Amyloid Fibrils

• DOI: 10.2210/pdb5KK3/pdb
• BMRB: 30121

• Classification: PROTEIN FIBRIL
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-06-20 Released: 2016-07-13 
• Deposition Author(s): Colvin, M.T., Silvers, R., Zhe Ni, Q., Can, T.V., Sergeyev, I., Rosay, M., Donovan, K.J., Michael, B., Wall, J., Linse, S., Griffin, R.G.
• Funding Organization(s): National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB), German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: SOLID-STATE NMR
• Conformers Submitted: 10 

Literature

Atomic Resolution Structure of Monomorphic A beta 42 Amyloid Fibrils.

Colvin, M.T., Silvers, R., Ni, Q.Z., Can, T.V., Sergeyev, I., Rosay, M., Donovan, K.J., Michael, B., Wall, J., Linse, S., Griffin, R.G.

(2016) J Am Chem Soc 138: 9663-9674

• PubMed: 27355699 
• DOI: 10.1021/jacs.6b05129
• Primary Citation of Related Structures:  
  5KK3


• PubMed Abstract: 
  

Amyloid-β (Aβ) is a 39-42 residue protein produced by the cleavage of the amyloid precursor protein (APP), which subsequently aggregates to form cross-β amyloid fibrils that are a hallmark of Alzheimer's disease (AD). The most prominent forms of Aβ are Aβ1-40 and Aβ1-42, which differ by two amino acids (I and A) at the C-terminus. However, Aβ42 is more neurotoxic and essential to the etiology of AD. Here, we present an atomic resolution structure of a monomorphic form of AβM01-42 amyloid fibrils derived from over 500 (13)C-(13)C, (13)C-(15)N distance and backbone angle structural constraints obtained from high field magic angle spinning NMR spectra. The structure (PDB ID: 5KK3 ) shows that the fibril core consists of a dimer of Aβ42 molecules, each containing four β-strands in a S-shaped amyloid fold, and arranged in a manner that generates two hydrophobic cores that are capped at the end of the chain by a salt bridge. The outer surface of the monomers presents hydrophilic side chains to the solvent. The interface between the monomers of the dimer shows clear contacts between M35 of one molecule and L17 and Q15 of the second. Intermolecular (13)C-(15)N constraints demonstrate that the amyloid fibrils are parallel in register. The RMSD of the backbone structure (Q15-A42) is 0.71 ± 0.12 Å and of all heavy atoms is 1.07 ± 0.08 Å. The structure provides a point of departure for the design of drugs that bind to the fibril surface and therefore interfere with secondary nucleation and for other therapeutic approaches to mitigate Aβ42 aggregation.

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Related Citations: 

• High resolution structural characterization of AB42 amyloid fibrils by magic angle spinning NMR.
  Colvin, M.T., Silvers, R., Frohm, B., Su, Y., Linse, S., Griffin, R.G.
  (2015) J Am Chem Soc 137: 7509

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Organizational Affiliation: 

Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-amyloid protein 42	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	42	Homo sapiens	Mutation(s): 0  Gene Names: APP, A4, AD1
UniProt & NIH Common Fund Data Resources
Find proteins for P05067 (Homo sapiens) Explore P05067  Go to UniProtKB:  P05067
PHAROS:  P05067

Experimental Data & Validation

Experimental Data

• Method: SOLID-STATE NMR
• Conformers Submitted: 10 
• OLDERADO: 5KK3 Olderado

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-06-20 
• Released Date: 2016-07-13 
Deposition Author(s): Colvin, M.T., Silvers, R., Zhe Ni, Q., Can, T.V., Sergeyev, I., Rosay, M., Donovan, K.J., Michael, B., Wall, J., Linse, S., Griffin, R.G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)	United States	EB-003151
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)	United States	EB-002026
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)	United States	EB-002804
German Research Foundation (DFG)	Germany	SI2105/1-1

Revision History  

• Version 1.0: 2016-07-13
  Type: Initial release
  
• Version 1.1: 2016-07-20
  Changes: Database references
• Version 1.2: 2016-08-17
  Changes: Database references
• Version 1.3: 2017-09-20
  Changes: Author supporting evidence, Structure summary
• Version 1.4: 2017-09-27
  Changes: Author supporting evidence
• Version 1.5: 2019-12-11
  Changes: Author supporting evidence, Data collection