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- EMDB-37416: Cryo-EM structure of Snf7 N-terminal domain in outer coils of spi... -

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Basic information

Entry
Database: EMDB / ID: EMD-37416
TitleCryo-EM structure of Snf7 N-terminal domain in outer coils of spiral polymers
Map data
Sample
  • Complex: Snf7 spiral polymers
    • Protein or peptide: SNF7 isoform 1
Keywordsmembrane fission / spiral polymers / N-terminal domain / "open" status / PROTEIN TRANSPORT
Function / homologyESCRT III complex / Snf7 family / Snf7 / late endosome to vacuole transport via multivesicular body sorting pathway / vesicle budding from membrane / multivesicular body / cytoplasmic side of plasma membrane / Vacuolar-sorting protein SNF7
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.1 Å
AuthorsLiu MD / Shen QT
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Three-dimensional architecture of ESCRT-III flat spirals on the membrane.
Authors: Mingdong Liu / Yunhui Liu / Tiefeng Song / Liuyan Yang / Lei Qi / Yu-Zhong Zhang / Yong Wang / Qing-Tao Shen /
Abstract: The endosomal sorting complexes required for transport (ESCRTs) are responsible for membrane remodeling in many cellular processes, such as multivesicular body biogenesis, viral budding, and ...The endosomal sorting complexes required for transport (ESCRTs) are responsible for membrane remodeling in many cellular processes, such as multivesicular body biogenesis, viral budding, and cytokinetic abscission. ESCRT-III, the most abundant ESCRT subunit, assembles into flat spirals as the primed state, essential to initiate membrane invagination. However, the three-dimensional architecture of ESCRT-III flat spirals remained vague for decades due to highly curved filaments with a small diameter and a single preferred orientation on the membrane. Here, we unveiled that yeast Snf7, a component of ESCRT-III, forms flat spirals on the lipid monolayers using cryogenic electron microscopy. We developed a geometry-constrained Euler angle-assigned reconstruction strategy and obtained moderate-resolution structures of Snf7 flat spirals with varying curvatures. Our analyses showed that Snf7 subunits recline on the membrane with N-terminal motifs α0 as anchors, adopt an open state with fused α2/3 helices, and bend α2/3 gradually from the outer to inner parts of flat spirals. In all, we provide the orientation and conformations of ESCRT-III flat spirals on the membrane and unveil the underlying assembly mechanism, which will serve as the initial step in understanding how ESCRTs drive membrane abscission.
History
DepositionSep 8, 2023-
Header (metadata) releaseMay 29, 2024-
Map releaseMay 29, 2024-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_37416.png

Downloads & links

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Map

FileDownload / File: emd_37416.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.0098
Minimum - Maximum-0.008741313 - 0.027756153
Average (Standard dev.)0.00008764938 (±0.0021356)
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: #1

Fileemd_37416_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_37416_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Snf7 spiral polymers

EntireName: Snf7 spiral polymers
Components
  • Complex: Snf7 spiral polymers
    • Protein or peptide: SNF7 isoform 1

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Supramolecule #1: Snf7 spiral polymers

SupramoleculeName: Snf7 spiral polymers / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: SNF7 isoform 1

MacromoleculeName: SNF7 isoform 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 27.020119 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MWSSLFGWTS SNAKNKESPT KAIVRLREHI NLLSKKQSHL RTQITNQENE ARIFLTKGNK VMAKNALKKK KTIEQLLSKV EGTMESMEQ QLFSIESANL NLETMRAMQE GAKAMKTIHS GLDIDKVDET MDEIREQVEL GDEISDAISR PLITGANEVD E DELDEELD ...String:
MWSSLFGWTS SNAKNKESPT KAIVRLREHI NLLSKKQSHL RTQITNQENE ARIFLTKGNK VMAKNALKKK KTIEQLLSKV EGTMESMEQ QLFSIESANL NLETMRAMQE GAKAMKTIHS GLDIDKVDET MDEIREQVEL GDEISDAISR PLITGANEVD E DELDEELD MLAQENANQE TSKIVNNNVN AAPISENKVS LPSVPSNKIK QSENSVKDGE EEEDEEDEDE KALRELQAEM GL

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

MicroscopeFEI TITAN 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: SPOT SCAN / 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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 175049
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD

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