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- EMDB-45883: Y20S (Sec18-Sec17-Sec9-Sso1-Snc1) EDTA - Class 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-45883
TitleY20S (Sec18-Sec17-Sec9-Sso1-Snc1) EDTA - Class 1
Map dataFor overall placement of SNARE spire and Sec17 adaptor molecules
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


inter-Golgi cisterna vesicle-mediated transport / Disinhibition of SNARE formation / vesicle fusion to plasma membrane / ascospore-type prospore assembly / Retrograde transport at the Trans-Golgi-Network / RHOQ GTPase cycle / vesicle fusion with Golgi apparatus / RHOB GTPase cycle / RHOA GTPase cycle / Golgi vesicle fusion to target membrane ...inter-Golgi cisterna vesicle-mediated transport / Disinhibition of SNARE formation / vesicle fusion to plasma membrane / ascospore-type prospore assembly / Retrograde transport at the Trans-Golgi-Network / RHOQ GTPase cycle / vesicle fusion with Golgi apparatus / RHOB GTPase cycle / RHOA GTPase cycle / Golgi vesicle fusion to target membrane / sporulation / cellular bud / Intra-Golgi traffic / trans-Golgi Network Vesicle Budding / prospore membrane / soluble NSF attachment protein activity / ascospore formation / vacuole fusion, non-autophagic / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPII-mediated vesicle transport / SNARE complex disassembly / Golgi to endosome transport / vesicle docking / SNAP receptor activity / SNARE complex / phosphatidic acid binding / vesicle fusion / Golgi to plasma membrane transport / cellular bud neck / intra-Golgi vesicle-mediated transport / Golgi to plasma membrane protein transport / mating projection tip / Golgi stack / phosphatidylinositol-3,4-bisphosphate binding / 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. / Vesicle-fusing ATPase / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Syntaxin ...Synaptobrevin/Vesicle-associated membrane protein / NSF attachment protein / Soluble NSF attachment protein, SNAP / Synaptobrevin signature. / Vesicle-fusing ATPase / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / 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: 3.89 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: To Be Published
Title: A conserved mechanism for universal SNARE recycling across cellular contexts
Authors: Khan YA / Brunger AT
History
DepositionJul 22, 2024-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: RCSB / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_45883.map.gz / Format: CCP4 / Size: 96.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFor overall placement of SNARE spire and Sec17 adaptor molecules
Voxel sizeX=Y=Z: 1.096 Å
Density
Contour LevelBy AUTHOR: 0.002
Minimum - Maximum-0.012318795 - 0.024338076
Average (Standard dev.)-0.0000034439206 (±0.0012478385)
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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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 / Details: Cleaved Sec18 / 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 / Details: TEV cleaved Sec17 / Number of copies: 2 / 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 / Details: Snc1p TEV cleaved / 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 / Details: Sso1 TEV cleaved / 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 / Details: Sec9 TEV cleaved / 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: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 41159
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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