8OG0 | pdb_00008og0

Crystal structure of MJF14-6-4-2 Fab fragment in complex with epitope peptide

• PDB DOI: https://doi.org/10.2210/pdb8OG0/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Oryctolagus cuniculus, Homo sapiens
• Expression System: Oryctolagus cuniculus
• Mutation(s): No 


• Deposited: 2023-03-17 Released: 2024-03-27 
• Deposition Author(s): Tars, K., Lieknina, I.
• Funding Organization(s): European Union (EU)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 
  0.231 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Structural basis of epitope recognition by anti-alpha-synuclein antibodies MJFR14-6-4-2.

Lieknina, I., Reimer, L., Pantelejevs, T., Lends, A., Jaudzems, K., El-Turabi, A., Gram, H., Hammi, A., Jensen, P.H., Tars, K.

(2024) NPJ Parkinsons Dis 10: 206-206

• PubMed: 39463404 
• DOI: https://doi.org/10.1038/s41531-024-00822-y
• Primary Citation Related Structures: 
  8OG0


• PubMed Abstract: 
  

  Alpha-synuclein (α-syn) inclusions in the brain are hallmarks of so-called Lewy body diseases. Lewy bodies contain mainly aggregated α-syn together with some other proteins. Monomeric α-syn lacks a well-defined three-dimensional structure, but it can aggregate into oligomeric and fibrillar amyloid species, which can be detected using specific antibodies. Here we investigate the aggregate specificity of monoclonal MJFR14-6-4-2 antibodies. We conclude that partial masking of epitope in unstructured monomer in combination with a high local concentration of epitopes is the main reason for MJFR14-6-4-2 selectivity towards aggregates. Based on the structural insight, we produced mutant α-syn that when fibrillated is unable to bind MJFR14-6-4-2. Using these fibrils as a tool for seeding cellular α-syn aggregation, provides superior signal/noise ratio for detection of cellular α-syn aggregates by MJFR14-6-4-2. Our data provide a molecular level understanding of specific recognition of toxic amyloid oligomers, which is critical for the development of inhibitors against synucleinopathies.

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Organizational Affiliation: 
• Latvian Biomedical Research and Study Centre, Ratsupites 1, k-1, LV-1067, Riga, Latvia.
University of Aarhus, Danish Research Institute of Translational Neuroscience DANDRITE and Department of Biomedicine, Aarhus, Denmark.
Latvian Institute of Organic Synthesis, Aizkraukles 21, LV-1006, Riga, Latvia.
University of Latvia, Jelgavas 1, LV-1004, Riga, Latvia.
University of Oxford, Jenner Institute, Nuffield Department of Medicine, OX3 7DQ, Oxford, UK.
University of Aarhus, Danish Research Institute of Translational Neuroscience DANDRITE and Department of Biomedicine, Aarhus, Denmark. [e-mail].
Latvian Biomedical Research and Study Centre, Ratsupites 1, k-1, LV-1067, Riga, Latvia. [e-mail].
University of Latvia, Jelgavas 1, LV-1004, Riga, Latvia. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 46.86 kDa 
• Atom Count: 3,447 
• Modeled Residue Count: 432 
• Deposited Residue Count: 443 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab fragment light chain	A [auth L]	216	Oryctolagus cuniculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab fragment heavy chain	B [auth H]	222	Oryctolagus cuniculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-synuclein	C [auth P]	5	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P37840 (Homo sapiens) Explore P37840  Go to UniProtKB:  P37840
PHAROS:  P37840 GTEx:  ENSG00000145335

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free:  0.231 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.484	α = 90
b = 66.7	β = 90
c = 167.167	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-03-27 
Deposition Author(s): Tars, K., Lieknina, I.

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Funding Organization	Location	Grant Number
European Union (EU)	European Union	OligoFIT

Revision History  

• Version 1.0: 2024-03-27
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Database references, Structure summary