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- EMDB-49833: NSF Mg2+ class 2 hexamer -

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Basic information

Entry
Database: EMDB / ID: EMD-49833
TitleNSF Mg2+ class 2 hexamer
Map data
Sample
  • Complex: NSF Mg2+ class 2
    • Protein or peptide: Vesicle-fusing ATPase
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsSNARE / NSF / Sec18 / AAA+ / TRANSLOCASE
Function / homology
Function and homology information


SNARE complex disassembly / ATP-dependent protein disaggregase activity / intra-Golgi vesicle-mediated transport / Golgi to plasma membrane protein transport / Golgi stack / vesicle-fusing ATPase / syntaxin-1 binding / positive regulation of receptor recycling / ionotropic glutamate receptor binding / SNARE binding ...SNARE complex disassembly / ATP-dependent protein disaggregase activity / intra-Golgi vesicle-mediated transport / Golgi to plasma membrane protein transport / Golgi stack / vesicle-fusing ATPase / syntaxin-1 binding / positive regulation of receptor recycling / ionotropic glutamate receptor binding / SNARE binding / PDZ domain binding / intracellular protein transport / potassium ion transport / positive regulation of protein catabolic process / midbody / protein kinase binding / protein-containing complex binding / ATP hydrolysis activity / ATP binding / metal ion binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
: / NSF, AAA+ ATPase lid domain / Vesicle-fusing ATPase / Cell division protein 48 (CDC48), N-terminal domain / 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 ...: / NSF, AAA+ ATPase lid domain / Vesicle-fusing ATPase / Cell division protein 48 (CDC48), N-terminal domain / 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
Vesicle-fusing ATPase
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsKhan YA / Brunger AT
Funding support United States, 2 items
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 20, 2025-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49833.png

Downloads & links

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Map

FileDownload / File: emd_49833.map.gz / Format: CCP4 / Size: 96.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 294 pix.
= 322.224 Å		1.1 Å/pix.
x 294 pix.
= 322.224 Å		1.1 Å/pix.
x 294 pix.
= 322.224 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.096 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.5605388 - 1.1875986
Average (Standard dev.)0.009990199 (±0.05902581)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions294294294
Spacing294294294
CellA=B=C: 322.224 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_49833_additional_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_49833_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49833_half_map_2.map
Projections & Slices
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Sample components

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Entire : NSF Mg2+ class 2

EntireName: NSF Mg2+ class 2
Components
  • Complex: NSF Mg2+ class 2
    • Protein or peptide: Vesicle-fusing ATPase
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: NSF Mg2+ class 2

SupramoleculeName: NSF Mg2+ class 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Cricetulus griseus (Chinese hamster)

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Macromolecule #1: Vesicle-fusing ATPase

MacromoleculeName: Vesicle-fusing ATPase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: vesicle-fusing ATPase
Source (natural)Organism: Cricetulus griseus (Chinese hamster)
Molecular weightTheoretical: 82.90743 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GAHMAGRSMQ AARCPTDELS LSNCAVVSEK DYQSGQHVIV RTSPNHKYIF TLRTHPSVVP GSVAFSLPQR KWAGLSIGQE IEVALYSFD KAKQCIGTMT IEIDFLQKKN IDSNPYDTDK MAAEFIQQFN NQAFSVGQQL VFSFNDKLFG LLVKDIEAMD P SILKGEPA ...String:
GAHMAGRSMQ AARCPTDELS LSNCAVVSEK DYQSGQHVIV RTSPNHKYIF TLRTHPSVVP GSVAFSLPQR KWAGLSIGQE IEVALYSFD KAKQCIGTMT IEIDFLQKKN IDSNPYDTDK MAAEFIQQFN NQAFSVGQQL VFSFNDKLFG LLVKDIEAMD P SILKGEPA SGKRQKIEVG LVVGNSQVAF EKAENSSLNL IGKAKTKENR QSIINPDWNF EKMGIGGLDK EFSDIFRRAF AS RVFPPEI VEQMGCKHVK GILLYGPPGC GKTLLARQIG KMLNAREPKV VNGPEILNKY VGESEANIRK LFADAEEEQR RLG ANSGLH IIIFDEIDAI CKQRGSMAGS TGVHDTVVNQ LLSKIDGVEQ LNNILVIGMT NRPDLIDEAL LRPGRLEVKM EIGL PDEKG RLQILHIHTA RMRGHQLLSA DVDIKELAVE TKNFSGAELE GLVRAAQSTA MNRHIKASTK VEVDMEKAES LQVTR GDFL ASLENDIKPA FGTNQEDYAS YIMNGIIKWG DPVTRVLDDG ELLVQQTKNS DRTPLVSVLL EGPPHSGKTA LAAKIA EES NFPFIKICSP DKMIGFSETA KCQAMKKIFD DAYKSQLSCV VVDDIERLLD YVPIGPRFSN LVLQALLVLL KKAPPQG RK LLIIGTTSRK DVLQEMEMLN AFSTTIHVPN IATGEQLLEA LELLGNFKDK ERTTIAQQVK GKKVWIGIKK LLMLIEMS L QMDPEYRVRK FLALLREEGA SPLDFD

UniProtKB: Vesicle-fusing ATPase

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 10 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -1.8 µm / Nominal defocus min: -0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 11844
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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