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- EMDB-48826: Y20S (Sec18-Sec17-Sec9-Sso1-Snc1) EDTA - Class 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-48826
TitleY20S (Sec18-Sec17-Sec9-Sso1-Snc1) EDTA - Class 2
Map data
Sample
  • Complex: Y20S complex EDTA
    • Protein or peptide: Vesicular-fusion protein SEC18
    • Protein or peptide: Alpha-soluble NSF attachment protein
    • Protein or peptide: Synaptobrevin homolog 1
    • Protein or peptide: Protein SSO1
    • Protein or peptide: Protein transport protein SEC9
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsSNARE / NSF / Sec18 / AAA+ / TRANSLOCASE
Function / homology
Function and homology information


Disinhibition of SNARE formation / vesicle fusion to plasma membrane / ascospore-type prospore assembly / inter-Golgi cisterna vesicle-mediated transport / RHOQ GTPase cycle / Retrograde transport at the Trans-Golgi-Network / RHOB GTPase cycle / RHOA GTPase cycle / Golgi vesicle fusion to target membrane / vesicle fusion with Golgi apparatus ...Disinhibition of SNARE formation / vesicle fusion to plasma membrane / ascospore-type prospore assembly / inter-Golgi cisterna vesicle-mediated transport / RHOQ GTPase cycle / Retrograde transport at the Trans-Golgi-Network / RHOB GTPase cycle / RHOA GTPase cycle / Golgi vesicle fusion to target membrane / vesicle fusion with Golgi apparatus / cellular bud / sporulation / trans-Golgi Network Vesicle Budding / prospore membrane / soluble NSF attachment protein activity / Intra-Golgi traffic / ascospore formation / vacuole fusion, non-autophagic / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / Golgi to endosome transport / COPII-mediated vesicle transport / SNARE complex disassembly / vesicle docking / SNAP receptor activity / SNARE complex / vesicle fusion / Golgi to plasma membrane transport / phosphatidic acid binding / cellular bud neck / intra-Golgi vesicle-mediated transport / mating projection tip / Golgi to plasma membrane protein transport / phosphatidylinositol-3,4-bisphosphate binding / Golgi stack / fungal-type vacuole membrane / retrograde transport, endosome to Golgi / phosphatidylinositol-3,5-bisphosphate binding / syntaxin binding / SNARE complex assembly / transport vesicle membrane / exocytosis / ATPase activator activity / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / phosphatidylinositol-4,5-bisphosphate binding / Neutrophil degranulation / endomembrane system / SNARE binding / cell periphery / macroautophagy / intracellular protein transport / trans-Golgi network / autophagy / endocytosis / molecular adaptor activity / endosome membrane / endosome / Golgi membrane / Golgi apparatus / ATP hydrolysis activity / ATP binding / plasma membrane / cytosol
Similarity search - Function
Synaptobrevin/Vesicle-associated membrane protein / NSF attachment protein / Soluble NSF attachment protein, SNAP / Synaptobrevin signature. / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Vesicle-fusing ATPase / Syntaxin ...Synaptobrevin/Vesicle-associated membrane protein / NSF attachment protein / Soluble NSF attachment protein, SNAP / Synaptobrevin signature. / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Vesicle-fusing ATPase / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / SNARE domain / Syntaxin / Syntaxin/epimorphin, conserved site / Syntaxin / epimorphin family signature. / SNARE / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology 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 / Tetratricopeptide-like helical domain superfamily / 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 / Synaptobrevin homolog 1 / Alpha-soluble NSF attachment protein / Protein SSO1 / Protein transport protein SEC9
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.91 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
DepositionJan 27, 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_48826.png

Downloads & links

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Map

FileDownload / File: emd_48826.map.gz / Format: CCP4 / Size: 96.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.096 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.00248
Minimum - Maximum-0.012194045 - 0.023467755
Average (Standard dev.)-0.000016334492 (±0.001280482)
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: #2

Fileemd_48826_additional_1.map
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Additional map: #1

Fileemd_48826_additional_2.map
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Half map: #2

Fileemd_48826_half_map_1.map
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Half map: #1

Fileemd_48826_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
    • Protein or peptide: Alpha-soluble NSF attachment protein
    • Protein or peptide: Synaptobrevin homolog 1
    • Protein or peptide: Protein SSO1
    • Protein or peptide: Protein transport protein SEC9
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Y20S complex EDTA

SupramoleculeName: Y20S complex EDTA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
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: Alpha-soluble NSF attachment protein

MacromoleculeName: Alpha-soluble NSF attachment protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 32.899828 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GMSDPVELLK RAEKKGVPSS GFMKLFSGSD SYKFEEAADL CVQAATIYRL RKELNLAGDS FLKAADYQKK AGNEDEAGNT YVEAYKCFK SGGNSVNAVD SLENAIQIFT HRGQFRRGAN FKFELGEILE NDLHDYAKAI DCYELAGEWY AQDQSVALSN K CFIKCADL ...String:
GMSDPVELLK RAEKKGVPSS GFMKLFSGSD SYKFEEAADL CVQAATIYRL RKELNLAGDS FLKAADYQKK AGNEDEAGNT YVEAYKCFK SGGNSVNAVD SLENAIQIFT HRGQFRRGAN FKFELGEILE NDLHDYAKAI DCYELAGEWY AQDQSVALSN K CFIKCADL KALDGQYIEA SDIYSKLIKS SMGNRLSQWS LKDYFLKKGL CQLAATDAVA AARTLQEGQS EDPNFADSRE SN FLKSLID AVNEGDSEQL SEHCKEFDNF MRLDKWKITI LNKIKESIQQ QEDDLL

UniProtKB: Alpha-soluble NSF attachment protein

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Macromolecule #3: Synaptobrevin homolog 1

MacromoleculeName: Synaptobrevin homolog 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 10.943198 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GASHMSSSTP FDPYALSEHD EERPQNVQSK SRTAELQAEI DDTVGIMRDN INKVAERGER LTSIEDKADN LAVSAQGFKR GANRVRKAM WYKDLKMK

UniProtKB: Synaptobrevin homolog 1

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Macromolecule #4: Protein SSO1

MacromoleculeName: Protein SSO1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 30.798027 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GASHMSYNNP YQLETPFEES YELDEGSSAI GAEGHDFVGF MNKISQINRD LDKYDHTINQ VDSLHKRLLT EVNEEQASHL RHSLDNFVA QATDLQFKLK NEIKSAQRDG IHDTNKQAQA ENSRQRFLKL IQDYRIVDSN YKEENKEQAK RQYMIIQPEA T EDEVEAAI ...String:
GASHMSYNNP YQLETPFEES YELDEGSSAI GAEGHDFVGF MNKISQINRD LDKYDHTINQ VDSLHKRLLT EVNEEQASHL RHSLDNFVA QATDLQFKLK NEIKSAQRDG IHDTNKQAQA ENSRQRFLKL IQDYRIVDSN YKEENKEQAK RQYMIIQPEA T EDEVEAAI SDVGGQQIFS QALLNANRRG EAKTALAEVQ ARHQELLKLE KSMAELTQLF NDMEELVIEQ QENVDVIDKN VE DAQLDVE QGVGHTDKAV KSARKARKNK IR

UniProtKB: Protein SSO1

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Macromolecule #5: Protein transport protein SEC9

MacromoleculeName: Protein transport protein SEC9 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 25.77792 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GASHIKFTKQ SSVASTRNTL KMAQDAERAG MNTLGMLGHQ SEQLNNVEGN LDLMKVQNKV ADEKVAELKK LNRSILAVHV SNPFNSKRR RREREEQLKN RKIEEKLMRE QTSQQLSQST QRIEGAMNAN NNISEVRERY QRKNVLEKAK RYQFENDEED D EMELEIDR ...String:
GASHIKFTKQ SSVASTRNTL KMAQDAERAG MNTLGMLGHQ SEQLNNVEGN LDLMKVQNKV ADEKVAELKK LNRSILAVHV SNPFNSKRR RREREEQLKN RKIEEKLMRE QTSQQLSQST QRIEGAMNAN NNISEVRERY QRKNVLEKAK RYQFENDEED D EMELEIDR NLDQIQQVSN RLKKMALTTG KELDSQQKRL NNIEESTDDL DINLHMNTNR LAGI

UniProtKB: Protein transport protein SEC9

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Macromolecule #6: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 2 / 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 #7: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 9 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, 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 reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.91 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 35723
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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