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- EMDB-49801: Y20S after Mg2+ (Sec18) - Class 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-49801
TitleY20S after Mg2+ (Sec18) - Class 2
Map data
Sample
  • Complex: Y20S complex EDTA
    • Protein or peptide: Vesicular-fusion protein SEC18
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: water
KeywordsSNARE / NSF / Sec18 / AAA+ / TRANSLOCASE
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
Vesicular-fusion protein SEC18
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.38 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 19, 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_49801.png

Downloads & links

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Map

FileDownload / File: emd_49801.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.98 Å/pix.
x 330 pix.
= 322.42 Å		0.98 Å/pix.
x 330 pix.
= 322.42 Å		0.98 Å/pix.
x 330 pix.
= 322.42 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97703 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.4226441 - 3.0691605
Average (Standard dev.)0.008370927 (±0.076687284)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions330330330
Spacing330330330
CellA=B=C: 322.4199 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_49801_additional_1.map
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Half map: #2

Fileemd_49801_half_map_1.map
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Half map: #1

Fileemd_49801_half_map_2.map
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Sample components

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Entire : Y20S complex EDTA

EntireName: Y20S complex EDTA
Components
  • Complex: Y20S complex EDTA
    • Protein or peptide: Vesicular-fusion protein SEC18
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: water

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Supramolecule #1: Y20S complex EDTA

SupramoleculeName: Y20S complex EDTA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Vesicular-fusion protein SEC18

MacromoleculeName: Vesicular-fusion protein SEC18 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 84.423297 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GAHMFKIPGF GKAAANHTPP DMTNMDTRTR HLKVSNCPNN SYALANVAAV SPNDFPNNIY IIIDNLFVFT TRHSNDIPPG TIGFNGNQR TWGGWSLNQD VQAKAFDLFK YSGKQSYLGS IDIDISFRAR GKAVSTVFDQ DELAKQFVRC YESQIFSPTQ Y LIMEFQGH ...String:
GAHMFKIPGF GKAAANHTPP DMTNMDTRTR HLKVSNCPNN SYALANVAAV SPNDFPNNIY IIIDNLFVFT TRHSNDIPPG TIGFNGNQR TWGGWSLNQD VQAKAFDLFK YSGKQSYLGS IDIDISFRAR GKAVSTVFDQ DELAKQFVRC YESQIFSPTQ Y LIMEFQGH FFDLKIRNVQ AIDLGDIEPT SAVATGIETK GILTKQTQIN FFKGRDGLVN LKSSNSLRPR SNAVIRPDFK FE DLGVGGL DKEFTKIFRR AFASRIFPPS VIEKLGISHV KGLLLYGPPG TGKTLIARKI GTMLNAKEPK IVNGPEILSK YVG SSEENI RNLFKDAEAE YRAKGEESSL HIIIFDELDS VFKQRGSRGD GTGVGDNVVN QLLAKMDGVD QLNNILVIGM TNRK DLIDS ALLRPGRFEV QVEIHLPDEK GRLQIFDIQT KKMRENNMMS DDVNLAELAA LTKNFSGAEI EGLVKSASSF AINKT VNIG KGATKLNTKD IAKLKVTRED FLNALNDVTP AFGISEEDLK TCVEGGMMLY SERVNSILKN GARYVRQVRE SDKSRL VSL LIHGPAGSGK TALAAEIALK SGFPFIRLIS PNELSGMSES AKIAYIDNTF RDAYKSPLNI LVIDSLETLV DWVPIGP RF SNNILQMLKV ALKRKPPQDR RLLIMTTTSA YSVLQQMDIL SCFDNEIAVP NMTNLDELNN VMIESNFLDD AGRVKVIN E LSRSCPNFNV GIKKTLTNIE TARHDEDPVN ELVELMTQSA

UniProtKB: Vesicular-fusion protein SEC18

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 6 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 6 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

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Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 6 / 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 #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 45 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 86542
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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