Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 47.70 kDa 
• Atom Count: 3540 
• Modelled Residue Count: 430 
• Deposited Residue Count: 441 
• Unique protein chains: 2

6CNR

aducanumab apo Fab

• PDB DOI: 10.2210/pdb6CNR/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2018-03-08 Released: 2018-05-02 
• Deposition Author(s): Arndt, J.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.239 
• R-Value Work: 0.211 
• R-Value Observed: 0.212 

Literature

Structural and kinetic basis for the selectivity of aducanumab for aggregated forms of amyloid-beta.

Arndt, J.W., Qian, F., Smith, B.A., Quan, C., Kilambi, K.P., Bush, M.W., Walz, T., Pepinsky, R.B., Bussiere, T., Hamann, S., Cameron, T.O., Weinreb, P.H.

(2018) Sci Rep 8: 6412-6412

• PubMed: 29686315 
• DOI: 10.1038/s41598-018-24501-0
• Primary Citation of Related Structures:  
  6CNR, 6CO3


• PubMed Abstract: 
  

Aducanumab, a human-derived antibody targeting amyloid-β (Aβ), is in Phase 3 clinical trials for the treatment of Alzheimer's disease. Biochemical and structural analyses show that aducanumab binds a linear epitope formed by amino acids 3-7 of the Aβ peptide. Aducanumab discriminates between monomers and oligomeric or fibrillar aggregates based on weak monovalent affinity, fast binding kinetics and strong avidity for epitope-rich aggregates. Direct comparative studies with analogs of gantenerumab, bapineuzumab and solanezumab demonstrate clear differentiation in the binding properties of these antibodies. The crystal structure of the Fab fragment of aducanumab bound to its epitope peptide reveals that aducanumab binds to the N terminus of Aβ in an extended conformation, distinct from those seen in structures with other antibodies that target this immunodominant epitope. Aducanumab recognizes a compact epitope that sits in a shallow pocket on the antibody surface. In silico analyses suggest that aducanumab interacts weakly with the Aβ monomer and may accommodate a variety of peptide conformations, further supporting its selectivity for Aβ aggregates. Our studies provide a structural rationale for the low affinity of aducanumab for non-pathogenic monomers and its greater selectivity for aggregated forms than is seen for other Aβ-targeting antibodies.

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Organizational Affiliation: 

Biogen, Cambridge, MA, USA. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aducanumab light chain	A [auth L]	214	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Aducanumab heavy chain	B [auth H]	227	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth H]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.239 
• R-Value Work: 0.211 
• R-Value Observed: 0.212 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.311	α = 90
b = 64.126	β = 95.85
c = 67.293	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-03-08 
• Released Date: 2018-05-02 
Deposition Author(s): Arndt, J.W.

Revision History  

• Version 1.0: 2018-05-02
  Type: Initial release
  
• Version 1.1: 2018-05-09
  Changes: Data collection, Database references