7OXN | pdb_00007oxn

Crystal Structure of TAP01 in complex with cyclised amyloid beta peptide

• PDB DOI: https://doi.org/10.2210/pdb7OXN/pdb

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


• Deposited: 2021-06-22 Released: 2022-06-29 
• Deposition Author(s): Hall, G., Cowan, R., Carr, M.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.265 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

Discovery of a novel pseudo beta-hairpin structure of N-truncated amyloid-beta for use as a vaccine against Alzheimer's disease.

Bakrania, P., Hall, G., Bouter, Y., Bouter, C., Beindorff, N., Cowan, R., Davies, S., Price, J., Mpamhanga, C., Love, E., Matthews, D., Carr, M.D., Bayer, T.A.

(2022) Mol Psychiatry 27: 840-848

• PubMed: 34776512 
• DOI: https://doi.org/10.1038/s41380-021-01385-7
• Primary Citation Related Structures: 
  7OW1, 7OXN


• PubMed Abstract: 
  

  One of the hallmarks of Alzheimer's disease (AD) are deposits of amyloid-beta (Aβ) protein in amyloid plaques in the brain. The Aβ peptide exists in several forms, including full-length Aβ1-42 and Aβ1-40 - and the N-truncated species, pyroglutamate Aβ3-42 and Aβ4-42, which appear to play a major role in neurodegeneration. We previously identified a murine antibody (TAP01), which binds specifically to soluble, non-plaque N-truncated Aβ species. By solving crystal structures for TAP01 family antibodies bound to pyroglutamate Aβ3-14, we identified a novel pseudo β-hairpin structure in the N-terminal region of Aβ and show that this underpins its unique binding properties. We engineered a stabilised cyclic form of Aβ1-14 (N-Truncated Amyloid Peptide AntibodieS; the 'TAPAS' vaccine) and showed that this adopts the same 3-dimensional conformation as the native sequence when bound to TAP01. Active immunisation of two mouse models of AD with the TAPAS vaccine led to a striking reduction in amyloid-plaque formation, a rescue of brain glucose metabolism, a stabilisation in neuron loss, and a rescue of memory deficiencies. Treating both models with the humanised version of the TAP01 antibody had similar positive effects. Here we report the discovery of a unique conformational epitope in the N-terminal region of Aβ, which offers new routes for active and passive immunisation against AD.

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Organizational Affiliation: 
• LifeArc, Centre for Therapeutics Discovery, Open Innovation Campus, Stevenage, UK. [e-mail].
Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, UK.
Department of Psychiatry and Psychotherapy, University Medical Center Göttingen (UMG), Georg-August-University, Göttingen, Germany.
Department of Nuclear Medicine, University Medical Center Göttingen (UMG), Georg-August-University, Göttingen, Germany.
Berlin Experimental Radionuclide Imaging Center (BERIC), Charité-Universitätsmedizin Berlin, Berlin, Germany.
LifeArc, Centre for Therapeutics Discovery, Open Innovation Campus, Stevenage, UK.
Mogrify, Bio-Innovation Centre, Cambridge Science Park, Cambridge, UK.
Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, UK. [e-mail].
Department of Psychiatry and Psychotherapy, University Medical Center Göttingen (UMG), Georg-August-University, Göttingen, Germany. [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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 48.58 kDa 
• Atom Count: 3,498 
• Modeled Residue Count: 441 
• Deposited Residue Count: 447 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TAP01 family antibody heavy chain	A [auth H]	219	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TAP01 family antibody light chain	B [auth K]	214	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Amyloid-beta precursor protein	C [auth A]	14	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
ZN	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	D [auth H]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
SMC	C [auth A]	CYS	Methylation	C4 H9 N O2 S

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.265 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.228 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.831	α = 90
b = 47.494	β = 90.955
c = 124.427	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-06-29 
Deposition Author(s): Hall, G., Cowan, R., Carr, M.D.

Revision History  

• Version 1.0: 2022-06-29
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary