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- PDB-9nue: Y20S after Mg2+ (Sec18) - Class 3 -

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Basic information

Entry
Database: PDB / ID: 9nue
TitleY20S after Mg2+ (Sec18) - Class 3
ComponentsVesicular-fusion protein SEC18
KeywordsTRANSLOCASE / SNARE / NSF / Sec18 / AAA+
Function / homology
Function and homology information


inter-Golgi cisterna vesicle-mediated transport / Retrograde transport at the Trans-Golgi-Network / vesicle fusion with Golgi apparatus / Intra-Golgi traffic / vacuole fusion, non-autophagic / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPII-mediated vesicle transport / SNARE complex disassembly / phosphatidic acid binding ...inter-Golgi cisterna vesicle-mediated transport / Retrograde transport at the Trans-Golgi-Network / vesicle fusion with Golgi apparatus / Intra-Golgi traffic / vacuole fusion, non-autophagic / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPII-mediated vesicle transport / SNARE complex disassembly / phosphatidic acid binding / intra-Golgi vesicle-mediated transport / mating projection tip / Golgi to plasma membrane protein transport / Golgi stack / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / SNARE binding / macroautophagy / Golgi apparatus / ATP hydrolysis activity / ATP binding / cytosol
Similarity search - Function
Vesicle-fusing ATPase / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 / CDC48 domain 2-like superfamily / Aspartate decarboxylase-like domain superfamily / AAA ATPase, AAA+ lid domain / AAA+ lid domain ...Vesicle-fusing ATPase / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 / CDC48 domain 2-like superfamily / Aspartate decarboxylase-like domain superfamily / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Vesicular-fusion protein SEC18
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsKhan, Y.A. / Brunger, A.T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)5R37MH063105 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)1F31MH134477 United States
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: SNARE disassembly requires Sec18/NSF side loading.
Authors: Yousuf A Khan / K Ian White / Richard A Pfuetzner / Bharti Singal / Luis Esquivies / Garvey Mckenzie / Fang Liu / Katherine DeLong / Ucheor B Choi / Elizabeth Montabana / Theresa Mclaughlin ...Authors: Yousuf A Khan / K Ian White / Richard A Pfuetzner / Bharti Singal / Luis Esquivies / Garvey Mckenzie / Fang Liu / Katherine DeLong / Ucheor B Choi / Elizabeth Montabana / Theresa Mclaughlin / William T Wickner / Axel T Brunger /
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- ...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.
History
DepositionMar 19, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vesicular-fusion protein SEC18
B: Vesicular-fusion protein SEC18
C: Vesicular-fusion protein SEC18
D: Vesicular-fusion protein SEC18
E: Vesicular-fusion protein SEC18
F: Vesicular-fusion protein SEC18
G: Vesicular-fusion protein SEC18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)597,24727
Polymers590,9637
Non-polymers6,28420
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Vesicular-fusion protein SEC18


Mass: 84423.297 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SEC18, YBR080C, YBR0736 / Production host: Escherichia coli (E. coli) / References: UniProt: P18759
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Y20S complex EDTA / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: -1800 nm / Nominal defocus min: -800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 91962 / Symmetry type: POINT

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