9PDB | pdb_00009pdb

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

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

  • Deposited: 2025-06-30 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)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Pre-fusion AAA+ remodeling of target-SNARE protein complexes 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.

(2024) bioRxiv 

  • DOI: https://doi.org/10.1101/2024.10.11.617886
  • 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, 9PFF, 9PFG

  • PubMed Abstract: 

    Membrane fusion is driven by SNARE complex formation across cellular contexts, including vesicle fusion during synaptic transmission. 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 show that the AAA+ protein NSF (N-ethylmaleimide sensitive factor) and SNAP (soluble NSF attachment protein) must act prior to fusion. We show that syntaxin clusters are conserved, that NSF colocalizes with them, and characterize SNARE populations within and near these clusters using cryo-EM. Supercomplexes of NSF, α-SNAP, and either a syntaxin tetramer or 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vesicle-fusing ATPase
A, B, C, D, E
A, B, C, D, E, F
747Cricetulus griseusMutation(s): 0 
Gene Names: NSF
EC: 3.6.4.6
UniProt
Find proteins for P18708 (Cricetulus griseus)
Explore P18708 
Go to UniProtKB:  P18708
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18708
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
unknown sequence14Cricetulus griseusMutation(s): 0 
Gene Names: NSF
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
H [auth A]
J [auth B]
M [auth C]
P [auth D]
S [auth E]
H [auth A],
J [auth B],
M [auth C],
P [auth D],
S [auth E],
T [auth E],
W [auth F]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
I [auth A],
K [auth B],
N [auth C],
Q [auth D],
X [auth F]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
PO4 (Subject of Investigation/LOI)
Query on PO4

Download Ideal Coordinates CCD File 
L [auth B],
O [auth C],
R [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
U [auth E],
V [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21
RECONSTRUCTIONcryoSPARC3.2.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--
Helen Hay Whitney FoundationUnited States--
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United StatesMH063105

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-06
    Type: Initial release