38DC | pdb_000038dc

X-ray Structure of the FAB Fragment of a GluA2-specific Murine Monoclonal Antibody 15F1

• PDB DOI: https://doi.org/10.2210/pdb38DC/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Spodoptera frugiperda
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2026-08-20 Released: 2026-11-04 
• Deposition Author(s): Nix, J., Dhandapani, G., Spangler, C.J., Pruneda, J.N., Gouaux, E.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.257 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: in silico

Literature

Programmable gold nanoparticle conjugates enable precise AMPA receptor localization at brain synapses by cryo-ET.

Spangler, C.J., Dhandapani, G., Matsui, A., Shiltseva, E.V., Nix, J., Pruneda, J.N., Elferich, J., Gouaux, E.

(2026) bioRxiv 

• PubMed: 42892767 
• DOI: https://doi.org/10.64898/2026.09.18.752772
• Primary Citation Related Structures: 
  38DC


• PubMed Abstract: 
  

  Cryo-electron tomography (cryo-ET) is a powerful approach to image cells, organelles, viruses and molecular assemblies. However, resolving smaller complexes and molecules is challenging and presents a roadblock to the broad application of cryo-ET. Gold nanoparticles (AuNPs) have been used to localize otherwise unidentifiable molecules and complexes in tomograms but are typically tethered to the target of interest via a flexible linker. As a result, the position of the AuNP does not directly define the location of the target. Here we attach AuNPs to Fab antibody fragments via cysteine residues on defined elements of secondary structure and show that the AuNPs are rigidly bound to the Fab. We use these Fab-AuNP conjugates to locate AMPA receptors and probe their conformation upon desensitization with sub nanometer resolution in tomograms derived from brain slice lamella. By harnessing small, homogeneous AuNPs with precise conjugation to a Fab, we have developed reagents that enable direct investigation of conformational states of previously unidentifiable biomolecules and complexes in tomograms.

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Organizational Affiliation: 
• Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA.
Howard Hughes Medical Institute, Oregon Health & Science University, Portland, OR 97239 USA.
RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.
Molecular Biology Consortium, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA.
Howard Hughes Medical Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 97.77 kDa 
• Atom Count: 6,912 
• Modeled Residue Count: 886 
• Deposited Residue Count: 898 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
15F1 Fab heavy chain	A, C	233	Spodoptera frugiperda	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
15F1 Fab light chain	B, D	216	Spodoptera frugiperda	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.257 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.461	α = 90
b = 64.277	β = 90
c = 204.89	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHENIX	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-11-04 
Deposition Author(s): Nix, J., Dhandapani, G., Spangler, C.J., Pruneda, J.N., Gouaux, E.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R37NS038631

Revision History  

• Version 1.0: 2026-11-04
  Type: Initial release