5W3P

ANTIBODY C706 IN COMPLEX WTH BETA-AMYLOID PEPTIDE 1-16

• PDB DOI: https://doi.org/10.2210/pdb5W3P/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2017-06-08 Released: 2017-09-20 
• Deposition Author(s): Teplyakov, A., Obmolova, G., Gilliland, G.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 0.236 
• R-Value Work: 0.198 
• R-Value Observed: 0.199 

Literature

A coiled conformation of amyloid-beta recognized by antibody C706.

Teplyakov, A., Obmolova, G., Gilliland, G.L.

(2017) Alzheimers Res Ther 9: 66-66

• PubMed: 28830506 
• DOI: https://doi.org/10.1186/s13195-017-0296-0
• Primary Citation of Related Structures:  
  5W3P


• PubMed Abstract: 
  

  β-Amyloid (Aβ) peptide is believed to play a pivotal role in the development of Alzheimer's disease. Passive immunization with anti-Aβ monoclonal antibodies may facilitate the clearance of Aβ in the brain and may thus prevent the downstream pathology. Antibodies targeting the immunodominant N-terminal epitope of Aβ and capable of binding both the plaques and soluble species have been most efficacious in animal models. Structural studies of such antibodies with bound Aβ peptides provided the basis for understanding the mechanisms of action and the differences in potency. To gain further insight into the structural determinants of antigen recognition and the preferential Aβ conformations, we determined the crystal structure of murine antibody C706 in complex with the N-terminal Aβ 1-16 peptide sequence.

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Organizational Affiliation: 

Janssen Research and Development, LLC, 1400 McKean Road, Spring House, PA, 19477, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Macromolecule Content

• Total Structure Weight: 49.07 kDa 
• Atom Count: 3,714 
• Modelled Residue Count: 444 
• Deposited Residue Count: 452 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody C706 Fab LIGHT CHAIN	A [auth L]	212	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody C706 Fab HEAVY CHAIN	B [auth H]	222	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Amyloid beta A4 protein	C [auth P]	18	Homo sapiens	Mutation(s): 2
UniProt & NIH Common Fund Data Resources
Find proteins for P05067 (Homo sapiens) Explore P05067  Go to UniProtKB:  P05067
PHAROS:  P05067 GTEx:  ENSG00000142192

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth L], G [auth H], I [auth P], J [auth P]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth L], F [auth L], H	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A [auth L]	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 0.236 
• R-Value Work: 0.198 
• R-Value Observed: 0.199 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.2	α = 90
b = 69.88	β = 90
c = 104.86	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
PHASER	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-09-20 
Deposition Author(s): Teplyakov, A., Obmolova, G., Gilliland, G.L.

Revision History  

• Version 1.0: 2017-09-20
  Type: Initial release
  
• Version 2.0: 2023-10-04
  Changes: Data collection, Database references, Polymer sequence, Refinement description