9PCX | pdb_00009pcx

22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a:SNAP-25), hydrolyzing, class 14

• PDB DOI: https://doi.org/10.2210/pdb9PCX/pdb
• EM Map EMD-71521: EMDB EMDataResource

• Classification: HYDROLASE
• Organism(s): Cricetulus griseus, Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-06-29 Released: 2025-08-06 
• Deposition Author(s): White, K.I., Brunger, A.T.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI), Helen Hay Whitney Foundation, National Institutes of Health/National Institute of Mental Health (NIH/NIMH)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.03 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Structural remodeling of target-SNARE protein complexes by NSF enables synaptic transmission.

White, K.I., Khan, Y.A., Qiu, K., Balaji, A., Couoh-Cardel, S., Esquivies, L., Pfuetzner, R.A., Diao, J., Brunger, A.T.

(2025) Nat Commun 16: 8371-8371

• PubMed: 40993127 
• DOI: https://doi.org/10.1038/s41467-025-62764-0
• Primary Citation of Related Structures:  
  9OJR, 9OJU, 9OJZ, 9OK3, 9OK5, 9OKC, 9OLJ, 9OLO, 9OM6, 9OMQ, 9PAF, 9PAG, 9PB9, 9PBA, 9PBF, 9PBV, 9PC3, 9PCX, 9PCZ, 9PD1, 9PD8, 9PDB, 9PDD, 9PF2, 9PFC, 9PFF, 9PFG


• PubMed Abstract: 
  

  Synaptic vesicles containing neurotransmitters fuse with the plasma membrane upon the arrival of an action potential at the active zone. Multiple proteins organize trans-SNARE complex assembly and priming, leading to fusion. One target membrane SNARE, syntaxin, forms nanodomains at the active zone, and another, SNAP-25, enters non-fusogenic complexes with it. Here, we reveal mechanistic details of AAA+ protein NSF (N-ethylmaleimide sensitive factor) and SNAP (soluble NSF attachment protein) action before fusion. We show that syntaxin clusters are conserved, that NSF colocalizes with them, and characterize SNARE populations that may exist within or near them using cryo-EM. Supercomplexes of NSF, α-SNAP, and either a syntaxin tetramer or one of two binary complexes of syntaxin-SNAP-25 reveal atomic details of SNARE processing and show how sequential ATP hydrolysis drives disassembly. These results suggest a functional role for syntaxin clusters as reservoirs and a corresponding role for NSF in syntaxin liberation and SNARE protein quality control preceding fusion.

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Organizational Affiliation: 
• Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA. [e-mail].
Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA. [e-mail].
Department of Structural Biology, Stanford University, Stanford, CA, USA. [e-mail].
Department of Photon Science, Stanford University, Stanford, CA, USA. [e-mail].
Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA. [e-mail].
Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA.
Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.
Department of Structural Biology, Stanford University, Stanford, CA, USA.
Department of Photon Science, Stanford University, Stanford, CA, USA.
Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
Department of Chemistry, Stanford University, Stanford, CA, USA.
Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA. [e-mail].
Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA. [e-mail].
Department of Structural Biology, Stanford University, Stanford, CA, USA. [e-mail].
Department of Photon Science, Stanford University, Stanford, CA, USA. [e-mail].
Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 14-mer - A4B4C2D2E2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 14-mer - A5B4C4D1 

Local Symmetry: Cyclic - C4  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - B4 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - D2E2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 915.17 kDa 
• Atom Count: 42,375 
• Modeled Residue Count: 5,376 
• Deposited Residue Count: 8,124 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vesicle-fusing ATPase	A, B, C, D, E, F	747	Cricetulus griseus	Mutation(s): 0  Gene Names: NSF EC: 3.6.4.6
UniProt
Find proteins for P18708 (Cricetulus griseus) Explore P18708  Go to UniProtKB:  P18708

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Syntaxin-1A	G [auth H], J [auth G]	267	Rattus norvegicus	Mutation(s): 0  Gene Names: Stx1a, Sap
UniProt
Find proteins for P32851 (Rattus norvegicus) Explore P32851  Go to UniProtKB:  P32851

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Synaptosomal-associated protein 25,Synaptosomal-associated protein 25, Alpha-soluble NSF attachment protein chimera	H [auth I], I [auth J], K, L, M, N	518	Rattus norvegicus	Mutation(s): 0  Gene Names: Snap25, Snap, Napa, Snapa
UniProt
Find proteins for P60881 (Rattus norvegicus) Explore P60881  Go to UniProtKB:  P60881

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP (Subject of Investigation/LOI)	P [auth A], Q [auth B], S [auth C], V [auth D], X [auth E], Y [auth E], Z [auth F]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)	AA [auth F], O [auth A], R [auth B], T [auth C], W [auth D]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
PO4 (Subject of Investigation/LOI)	U [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.03 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21
RECONSTRUCTION	cryoSPARC	3.2.0

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-06 
Deposition Author(s): White, K.I., Brunger, A.T.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--
Helen Hay Whitney Foundation	United States	--
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)	United States	MH063105

Revision History  

• Version 1.0: 2025-08-06
  Type: Initial release
  
• Version 1.1: 2025-10-08
  Changes: Data collection, Database references