9NUE | pdb_00009nue

Y20S after Mg2+ (Sec18) - Class 3

• PDB DOI: https://doi.org/10.2210/pdb9NUE/pdb
• EM Map EMD-49802: EMDB EMDataResource

• Classification: TRANSLOCASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-03-19 Released: 2025-10-01 
• Deposition Author(s): Khan, Y.A., Brunger, A.T.
• Funding Organization(s): National Institutes of Health/National Institute of Mental Health (NIH/NIMH)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.36 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

SNARE disassembly requires Sec18/NSF side loading.

Khan, Y.A., White, K.I., Pfuetzner, R.A., Singal, B., Esquivies, L., Mckenzie, G., Liu, F., DeLong, K., Choi, U.B., Montabana, E., Mclaughlin, T., Wickner, W.T., Brunger, A.T.

(2025) Nat Struct Mol Biol 32: 1708-1720

• PubMed: 40604310 
• DOI: https://doi.org/10.1038/s41594-025-01590-w
• Primary Citation of Related Structures:  
  9CRU, 9CRX, 9N22, 9NG2, 9NLU, 9NLW, 9NLY, 9NLZ, 9NM1, 9NUD, 9NUE, 9NUZ, 9NV0, 9NV1, 9NV9, 9NVD


• PubMed Abstract: 
  

  SNARE (soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein receptor) proteins drive membrane fusion at different cell compartments as their core domains zipper into a parallel four-helix bundle. After fusion, these bundles are disassembled by the AAA+ (ATPase associated with diverse cellular activities) protein Sec18/NSF and its adaptor Sec17/α-SNAP to make them available for subsequent rounds of membrane fusion. SNARE domains are often flanked by C-terminal transmembrane or N-terminal domains. Previous structures of the NSF-α-SNAP-SNARE complex revealed binding to the D1 ATPase pore, posing a topological constraint as SNARE transmembrane domains would prevent complete substrate threading as suggested for other AAA+ systems. Using mass spectrometry in yeast cells, we show N-terminal SNARE domain interactions with Sec18, exacerbating this topological issue. We present cryo-electron microscopy (cryo-EM) structures of a yeast SNARE complex, Sec18 and Sec17 in a nonhydrolyzing condition, which show SNARE Sso1 threaded through the D1 and D2 ATPase rings of Sec18, with its folded, N-terminal Habc domain interacting with the D2 ring. This domain does not unfold during Sec18/NSF activity. Cryo-EM structures under hydrolyzing conditions revealed substrate-released and substrate-free states of Sec18 with a coordinated opening in the side of the ATPase rings. Thus, Sec18/NSF operates by substrate side loading and unloading topologically constrained SNARE substrates.

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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].
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.
Stanford Cryo-Electron Microscopy Center (cEMc), Stanford University, Palo Alto, CA, USA.
Stanford University Mass Spectrometry, Stanford University, Palo Alto, CA, USA.
Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, Germany.
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 7-mer - A6B1 Pseudo Symmetry: Cyclic - C7  (Explore in 3D)
Pseudo Stoichiometry: Homo 7-mer - A7 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 597.25 kDa 
• Atom Count: 26,280 
• Modeled Residue Count: 3,327 
• Deposited Residue Count: 5,327 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vesicular-fusion protein SEC18	A, B, C, D, E, F, G	761	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: SEC18, YBR080C, YBR0736
UniProt
Find proteins for P18759 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P18759  Go to UniProtKB:  P18759

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.36 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-01 
Deposition Author(s): Khan, Y.A., Brunger, A.T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)	United States	5R37MH063105
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)	United States	1F31MH134477

Revision History  

• Version 1.0: 2025-10-01
  Type: Initial release