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- PDB-9jsd: Cryo-EM structure of Snf7 linker extension -

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Basic information

Entry
Database: PDB / ID: 9jsd
TitleCryo-EM structure of Snf7 linker extension
ComponentsVacuolar-sorting protein SNF7
KeywordsPROTEIN TRANSPORT / membrane fission / ring polymers / N-terminal domain / "open" status
Function / homology
Function and homology information


Sealing of the nuclear envelope (NE) by ESCRT-III / intralumenal vesicle formation / Macroautophagy / peroxisome organization / Endosomal Sorting Complex Required For Transport (ESCRT) / ESCRT III complex / late endosome to vacuole transport via multivesicular body sorting pathway / ATP export / vesicle budding from membrane / late endosome to vacuole transport ...Sealing of the nuclear envelope (NE) by ESCRT-III / intralumenal vesicle formation / Macroautophagy / peroxisome organization / Endosomal Sorting Complex Required For Transport (ESCRT) / ESCRT III complex / late endosome to vacuole transport via multivesicular body sorting pathway / ATP export / vesicle budding from membrane / late endosome to vacuole transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / reticulophagy / multivesicular body / cytoplasmic side of plasma membrane / nuclear envelope / protein transport / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Vacuolar-sorting protein SNF7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.37 Å
AuthorsShen, Q.T. / Liu, M.D.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: Cryo-EM structure of Snf7 linker extension
Authors: Shen, Q.T. / Liu, M.D.
History
DepositionSep 30, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 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

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Assembly

Deposited unit
A: Vacuolar-sorting protein SNF7


Theoretical massNumber of molelcules
Total (without water)27,8761
Polymers27,8761
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Vacuolar-sorting protein SNF7 / DOA4-independent degradation protein 1 / Sucrose nonfermenting protein 7 / Vacuolar protein-sorting- ...DOA4-independent degradation protein 1 / Sucrose nonfermenting protein 7 / Vacuolar protein-sorting-associated protein 32


Mass: 27875.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: SNF7, DID1, VPS32, YLR025W / Production host: Escherichia coli (E. coli) / References: UniProt: P39929
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: Snf7-ins15G ring polymers / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
 (yeast)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.6
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: 2400 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 7.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 199543 / Symmetry type: POINT

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