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- EMDB-61770: Cryo-EM structure of Snf7 linker extension -

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Basic information

Entry
Database: EMDB / ID: EMD-61770
TitleCryo-EM structure of Snf7 linker extension
Map data
Sample
  • Complex: Snf7-ins15G ring polymers
    • Protein or peptide: Vacuolar-sorting protein SNF7
Keywordsmembrane fission / ring polymers / N-terminal domain / "open" status / PROTEIN TRANSPORT
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 / cytoplasm / cytosol
Similarity search - Function
Vacuolar-sorting protein SNF7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c)
 (yeast) / Saccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.37 Å
AuthorsShen QT / Liu MD
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: Cryo-EM structure of Snf7 linker extension
Authors: Shen QT / Liu MD
History
DepositionSep 30, 2024-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61770.png

Downloads & links

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Map

FileDownload / File: emd_61770.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 160 pix.
= 169.6 Å		1.06 Å/pix.
x 160 pix.
= 169.6 Å		1.06 Å/pix.
x 160 pix.
= 169.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0087
Minimum - Maximum-0.0055876435 - 0.024177443
Average (Standard dev.)0.00029454546 (±0.0018446266)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 169.59999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61770_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61770_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Snf7-ins15G ring polymers

EntireName: Snf7-ins15G ring polymers
Components
  • Complex: Snf7-ins15G ring polymers
    • Protein or peptide: Vacuolar-sorting protein SNF7

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Supramolecule #1: Snf7-ins15G ring polymers

SupramoleculeName: Snf7-ins15G ring polymers / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
 (yeast)

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Macromolecule #1: Vacuolar-sorting protein SNF7

MacromoleculeName: Vacuolar-sorting protein SNF7 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 27.875887 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MWSSLFGWTS SNAKNKESPT KAIVRLREHI NLLSKKQSHL RTQITNQENE ARIFLTKGNK VMAKNALKKK KTIEQLLSKV EGTMESMEQ QLFSIESANL NLETMRAMQE GAKAMKTIHS GLDIDKVDET MDEIREQVEL GDEISDAISR PGGGGGGGGG G GGGGGLIT ...String:
MWSSLFGWTS SNAKNKESPT KAIVRLREHI NLLSKKQSHL RTQITNQENE ARIFLTKGNK VMAKNALKKK KTIEQLLSKV EGTMESMEQ QLFSIESANL NLETMRAMQE GAKAMKTIHS GLDIDKVDET MDEIREQVEL GDEISDAISR PGGGGGGGGG G GGGGGLIT GANEVDEDEL DEELDMLAQE NANQETSKIV NNNVNAAPIS ENKVSLPSVP SNKIKQSENS VKDGEEEEDE ED EDEKALR ELQAEMGL

UniProtKB: Vacuolar-sorting protein SNF7

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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: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: 2.4 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.37 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 199543
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD

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