6MDP | pdb_00006mdp

The D1 and D2 domain rings of NSF engaging the SNAP-25 N-terminus within the 20S supercomplex (focused refinement on D1/D2 rings, class 2)

PDB DOI: https://doi.org/10.2210/pdb6MDP/pdb
EM Map EMD-9103: EMDB EMDataResource

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

Deposited: 2018-09-04 Released: 2018-09-19
Deposition Author(s): White, K.I., Zhao, M., Brunger, A.T.
Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.80 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

PubMed: 30198481 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.7554/eLife.38888
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 541.99 kDa
Atom Count: 22,433
Modeled Residue Count: 2,832
Deposited Residue Count: 4,815
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vesicle-fusing ATPase	A, B, C, D, E A, B, C, D, E, F	768	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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P18708
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Synaptosomal-associated protein 25	G [auth H]	207	Rattus norvegicus	Mutation(s): 0 Gene Names: Snap25, Snap
UniProt
Find proteins for P60881 (Rattus norvegicus) Explore P60881 Go to UniProtKB: P60881
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60881
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain N [auth D] SDF format, chain P [auth E] SDF format, chain R [auth F] SDF format, chain O [auth D] SDF format, chain M [auth C] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth A] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] MOL2 format, chain P [auth E] MOL2 format, chain R [auth F] MOL2 format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D] mmCIF format, chain P [auth E] mmCIF format, chain R [auth F] mmCIF format, chain O [auth D] mmCIF format, chain M [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A]	I [auth A] J [auth B] K [auth B] L [auth C] M [auth C] I [auth A], J [auth B], K [auth B], L [auth C], M [auth C], N [auth D], O [auth D], P [auth E], R [auth F]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth E] Focus chain R [auth F] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth E] Focus chain R [auth F]
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain Q [auth E] MOL2 format, chain H [auth A] MOL2 format, chain Q [auth E] mmCIF format, chain H [auth A] mmCIF format, chain Q [auth E]	H [auth A], Q [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain H [auth A] Focus chain Q [auth E] Interactions & Density Focus chain H [auth A] Focus chain Q [auth E]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	Coot
RECONSTRUCTION	RELION	2.1

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-09-19

Deposition Author(s):

White, K.I.

Zhao, M.

Brunger, A.T.

Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	R37MH63105

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