6MDN

The 20S supercomplex engaging the SNAP-25 N-terminus (class 2)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural principles of SNARE complex recognition by the AAA+ protein NSF.

White, K.I.Zhao, M.Choi, U.B.Pfuetzner, R.A.Brunger, A.T.

(2018) Elife 7

  • DOI: https://doi.org/10.7554/eLife.38888
  • Primary Citation of Related Structures:  
    6MDM, 6MDN, 6MDO, 6MDP

  • PubMed Abstract: 

    The recycling of SNARE proteins following complex formation and membrane fusion is an essential process in eukaryotic trafficking. A highly conserved AAA+ protein, NSF ( N -ethylmaleimide sensitive factor) and an adaptor protein, SNAP (soluble NSF attachment protein), disassemble the SNARE complex. We report electron-cryomicroscopy structures of the complex of NSF, αSNAP, and the full-length soluble neuronal SNARE complex (composed of syntaxin-1A, synaptobrevin-2, SNAP-25A) in the presence of ATP under non-hydrolyzing conditions at ~3.9 Å resolution. These structures reveal electrostatic interactions by which two αSNAP molecules interface with a specific surface of the SNARE complex. This interaction positions the SNAREs such that the 15 N-terminal residues of SNAP-25A are loaded into the D1 ring pore of NSF via a spiral pattern of interactions between a conserved tyrosine NSF residue and SNAP-25A backbone atoms. This loading process likely precedes ATP hydrolysis. Subsequent ATP hydrolysis then drives complete disassembly.


  • Organizational Affiliation

    Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vesicle-fusing ATPase
A, B, C, D, E
A, B, C, D, E, F
768Cricetulus griseusMutation(s): 0 
Gene Names: NSF
EC: 3.6.4.6
UniProt
Find proteins for P18708 (Cricetulus griseus)
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Go to UniProtKB:  P18708
Entity Groups  
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UniProt GroupP18708
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Synaptosomal-associated protein 25G [auth H]207Rattus norvegicusMutation(s): 0 
Gene Names: Snap25Snap
UniProt
Find proteins for P60881 (Rattus norvegicus)
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Go to UniProtKB:  P60881
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UniProt GroupP60881
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Syntaxin-1AH [auth I]256Rattus norvegicusMutation(s): 0 
Gene Names: Stx1aSap
UniProt
Find proteins for P32851 (Rattus norvegicus)
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UniProt GroupP32851
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Vesicle-associated membrane protein 2I [auth J]117Rattus norvegicusMutation(s): 0 
Gene Names: Vamp2Syb2
UniProt
Find proteins for P63045 (Rattus norvegicus)
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UniProt GroupP63045
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-soluble NSF attachment proteinJ [auth K],
K [auth L]
313Rattus norvegicusMutation(s): 0 
Gene Names: NapaSnapSnapa
UniProt
Find proteins for P54921 (Rattus norvegicus)
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UniProt GroupP54921
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
L [auth A]
N [auth B]
O [auth B]
P [auth C]
Q [auth C]
L [auth A],
N [auth B],
O [auth B],
P [auth C],
Q [auth C],
R [auth D],
S [auth D],
T [auth E],
V [auth F]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
Query on ADP

Download Ideal Coordinates CCD File 
M [auth A],
U [auth E]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
MODEL REFINEMENTCoot
RECONSTRUCTIONRELION2.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesR37MH63105

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2018-09-26
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence, Other
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Refinement description