7LZ6 | pdb_00007lz6

The Cryo-EM structure of a complex between GAD65 and b96.11 Fab

• PDB DOI: https://doi.org/10.2210/pdb7LZ6/pdb
• EM Map EMD-23603: EMDB EMDataResource

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


• Deposited: 2021-03-09 Released: 2024-10-30 
• Deposition Author(s): Reboul, C.F., Le, S.N., Williams, D.E., Buckle, A.M.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 7.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure and dynamics of GAD65 in complex with an autoimmune polyendocrine syndrome type 2-associated autoantibody.

Stander, S.H.D., Reboul, C.F., Le, S.N., Williams, D.E., Chandler, P.G., Costa, M.G.S., Hoke, D.E., Jimma, J.D.T., Fodor, J., Fenalti, G., Mannering, S.I., Porebski, B.T., Schofield, P., Christ, D., Buckle, M., McGowan, S., Elmlund, D., Rand, K.D., Buckle, A.M.

(2025) Nat Commun 16: 2275-2275

• PubMed: 40055307 
• DOI: https://doi.org/10.1038/s41467-025-57492-4
• Primary Citation of Related Structures:  
  7LZ6, 9D7Y


• PubMed Abstract: 
  

  The enzyme glutamate decarboxylase (GAD) produces the neurotransmitter GABA, using pyridoxal-5'-phosphate (PLP). GAD exists as two isoforms, GAD65 and GAD67. Only GAD65 acts as a major autoantigen, frequently implicated in type 1 diabetes and other autoimmune diseases. Here we characterize the structure and dynamics of GAD65 and its interaction with the autoimmune polyendocrine syndrome type 2-associated autoantibody b96.11. Using hydrogen-deuterium exchange mass spectrometry (HDX), X-ray crystallography, cryo-electron microscopy, and computational approaches, we examine the conformational dynamics of apo- and holoGAD65 and the GAD65-autoantibody complex. HDX reveals local dynamics accompanying autoinactivation, with the catalytic loop promoting collective motions at the CTD-PLP domain interface. In the GAD65-b96.11 complex, heavy chain CDRs dominate the interaction, with a long CDRH3 bridging the GAD65 dimer via electrostatic interactions with the ₂₆₀ PEVKEK ₂₆₅ motif. This bridging links structural elements controlling GAD65's conformational flexibility to its autoantigenicity. Thus, intrinsic dynamics, rather than sequence differences within epitopes, appear to be responsible for the contrasting autoantigenicities of GAD65 and GAD67. Our findings elucidate the structural and dynamic factors that govern the varying autoantibody reactivities of GAD65 and GAD67, offering a revised rationale for the autoimmune response to GAD65.

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Organizational Affiliation: 
• Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark.
Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia.
National Institutes of Health, National Cancer Institute-Frederick Campus, Fredrick, MD, USA.
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
Programa de Computação Científica, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil.
The Centre for Brain, Mind and Markets, The University of Melbourne, Melbourne, VIC, Australia.
Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, Fitzroy, Melbourne, VIC, Australia.
Garvan Institute of Medical Research, UNSW Sydney, Darlinghurst, NSW, Australia.
LBPA, ENS de Paris-Saclay, UMR 8113 CNRS, Université Paris-Saclay 4, Gif-sur-Yvette, France.
Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark. [e-mail].
Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia. [e-mail].
San Diego Biomedical Research Institute, San Diego, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry, surface plasmon resonance

Macromolecule Content 

• Total Structure Weight: 208.34 kDa 
• Atom Count: 14,638 
• Modeled Residue Count: 1,884 
• Deposited Residue Count: 1,884 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate decarboxylase 2	A, B	497	Homo sapiens	Mutation(s): 0  Gene Names: GAD2, GAD65 EC: 4.1.1.15
UniProt & NIH Common Fund Data Resources
Find proteins for Q05329 (Homo sapiens) Explore Q05329  Go to UniProtKB:  Q05329
PHAROS:  Q05329 GTEx:  ENSG00000136750

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
b96.11 Fab heavy chain	C, E	228	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
b96.11 Fab light chain	D, F	217	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 7.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2024-10-30 
Deposition Author(s): Reboul, C.F., Le, S.N., Williams, D.E., Buckle, A.M.

Revision History  

• Version 1.0: 2024-10-30
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection
• Version 1.2: 2025-07-16
  Changes: Data collection, Database references