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- EMDB-10137: Refined, asymmetrically masked double-stranded helical ESCRT-III ... -

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Basic information

Entry
Database: EMDB / ID: EMD-10137
TitleRefined, asymmetrically masked double-stranded helical ESCRT-III filament formed from Snf7/Vps24/Vps2 on helical lipid bicelle
Map dataRefined, asymmetrically masked double-stranded helical ESCRT-III filament formed from Snf7/Vps24/Vps2 on helical lipid bicelle
Sample
  • Complex: Double-stranded helical ESCRT-III filament formed from Snf7/Vps24/Vps2 on a helical bicelle
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodhelical reconstruction / cryo EM / Resolution: 11.3 Å
AuthorsFrost A / Johnson I / Talledge N
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research ResourcesS10OD020054 United States
National Institutes of Health/National Center for Research Resources5P50GM082545-12 United States
National Institutes of Health/National Center for Research Resources1S10OD021741 United States
Howard Hughes Medical Institute United States
CitationJournal: Nat Commun / Year: 2020
Title: Anisotropic ESCRT-III architecture governs helical membrane tube formation.
Authors: Joachim Moser von Filseck / Luca Barberi / Nathaniel Talledge / Isabel E Johnson / Adam Frost / Martin Lenz / Aurélien Roux /
Abstract: ESCRT-III proteins assemble into ubiquitous membrane-remodeling polymers during many cellular processes. Here we describe the structure of helical membrane tubes that are scaffolded by bundled ESCRT- ...ESCRT-III proteins assemble into ubiquitous membrane-remodeling polymers during many cellular processes. Here we describe the structure of helical membrane tubes that are scaffolded by bundled ESCRT-III filaments. Cryo-ET reveals how the shape of the helical membrane tube arises from the assembly of two distinct bundles of helical filaments that have the same helical path but bind the membrane with different interfaces. Higher-resolution cryo-EM of filaments bound to helical bicelles confirms that ESCRT-III filaments can interact with the membrane through a previously undescribed interface. Mathematical modeling demonstrates that the interface described above is key to the mechanical stability of helical membrane tubes and helps infer the rigidity of the described protein filaments. Altogether, our results suggest that the interactions between ESCRT-III filaments and the membrane could proceed through multiple interfaces, to provide assembly on membranes with various shapes, or adapt the orientation of the filaments towards the membrane during membrane remodeling.
History
DepositionJul 20, 2019-
Header (metadata) releaseJun 3, 2020-
Map releaseJun 3, 2020-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.205
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.205
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10137.png

Downloads & links

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Map

FileDownload / File: emd_10137.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRefined, asymmetrically masked double-stranded helical ESCRT-III filament formed from Snf7/Vps24/Vps2 on helical lipid bicelle
Voxel sizeX=Y=Z: 2.76 Å
Density
Contour LevelBy AUTHOR: 0.205 / Movie #1: 0.205
Minimum - Maximum-0.084894784 - 0.3705108
Average (Standard dev.)0.0075001447 (±0.035519354)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 607.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.762.762.76
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z607.200607.200607.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.0850.3710.008

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Supplemental data

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Additional map: Refined, unmasked double-stranded helical ESCRT-III filament formed from...

Fileemd_10137_additional.map
AnnotationRefined, unmasked double-stranded helical ESCRT-III filament formed from Snf7/Vps24/Vps2 on helical lipid bicelle
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Refined, unmasked double-stranded helical ESCRT-III filament formed from...

Fileemd_10137_additional_1.map
AnnotationRefined, unmasked double-stranded helical ESCRT-III filament formed from Snf7/Vps24/Vps2 on helical lipid bicelle
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_10137_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_10137_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 : Double-stranded helical ESCRT-III filament formed from Snf7/Vps24...

EntireName: Double-stranded helical ESCRT-III filament formed from Snf7/Vps24/Vps2 on a helical bicelle
Components
  • Complex: Double-stranded helical ESCRT-III filament formed from Snf7/Vps24/Vps2 on a helical bicelle

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Supramolecule #1: Double-stranded helical ESCRT-III filament formed from Snf7/Vps24...

SupramoleculeName: Double-stranded helical ESCRT-III filament formed from Snf7/Vps24/Vps2 on a helical bicelle
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightExperimental: 30 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 67.2 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Segment selectionNumber selected: 35087 / Software - Name: RELION (ver. 3.0)
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 10.6 Å
Applied symmetry - Helical parameters - Δ&Phi: 6.7 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 11.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 35087
FSC plot (resolution estimation)

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