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- PDB-9cru: Y20S (Sec18-Sec17-Sec9-Sso1-Snc1) EDTA - Class 1 -

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Basic information

Entry
Database: PDB / ID: 9cru
TitleY20S (Sec18-Sec17-Sec9-Sso1-Snc1) EDTA - Class 1
Components
  • Alpha-soluble NSF attachment protein
  • Protein SSO1
  • Protein transport protein SEC9
  • Synaptobrevin homolog 1
  • Vesicular-fusion protein SEC18
KeywordsTRANSLOCASE / SNARE / NSF / Sec18 / AAA+
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
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.89 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: To Be Published
Title: A conserved mechanism for universal SNARE recycling across cellular contexts
Authors: Khan, Y.A. / Brunger, A.T.
History
DepositionJul 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Additional map / Part number: 3 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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: Alpha-soluble NSF attachment protein
H: Alpha-soluble NSF attachment protein
J: Synaptobrevin homolog 1
K: Protein SSO1
L: Protein transport protein SEC9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)645,27822
Polymers639,85911
Non-polymers5,41911
Water00
1


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

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Components

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Protein , 5 types, 11 molecules ABCDEFGHJKL

#1: Protein
Vesicular-fusion protein SEC18


Mass: 84423.297 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Cleaved Sec18
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SEC18, YBR080C, YBR0736 / Production host: Escherichia coli (E. coli) / References: UniProt: P18759
#2: Protein Alpha-soluble NSF attachment protein / SNAP-alpha / N-ethylmaleimide-sensitive factor attachment protein alpha / Vesicular-fusion protein ...SNAP-alpha / N-ethylmaleimide-sensitive factor attachment protein alpha / Vesicular-fusion protein SEC17 / alpha-SNAP chaperone


Mass: 32899.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: TEV cleaved Sec17
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SEC17, YBL050W, YBL0505, YBL0517 / Production host: Escherichia coli (E. coli) / References: UniProt: P32602
#3: Protein Synaptobrevin homolog 1


Mass: 10943.198 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Snc1p TEV cleaved
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SNC1, YAL030W / Production host: Escherichia coli (E. coli) / References: UniProt: P31109
#4: Protein Protein SSO1


Mass: 30798.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Sso1 TEV cleaved
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SSO1, YPL232W, P1405 / Production host: Escherichia coli (E. coli) / References: UniProt: P32867
#5: Protein Protein transport protein SEC9


Mass: 25777.920 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Sec9 TEV cleaved
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SEC9, HSS7, YGR009C / Production host: Escherichia coli (E. coli) / References: UniProt: P40357

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Non-polymers , 2 types, 11 molecules

#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#7: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM

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Details

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-#5 / 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: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41159 / Num. of class averages: 1 / Symmetry type: POINT

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