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- EMDB-10138: Segment of helical membrane tube with longitudinal ESCRT-III fila... -

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Basic information

Entry
Database: EMDB / ID: EMD-10138
TitleSegment of helical membrane tube with longitudinal ESCRT-III filaments with different binding modes formed from Snf7/Vps24/Vps2
Map dataSegment of helical membrane tube with longitudinal ESCRT-III filaments with different binding modes formed from Snf7/Vps24/Vps2
Sample
  • Complex: Segment of helical membrane tube with longitudinal ESCRT-III filaments with different binding modes formed from Snf7/Vps24/Vps2
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 31.9 Å
AuthorsMoser von Filseck J / Roux A
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
European UnionH2020 Grant # 653706 PID:6073 Switzerland
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: 1.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10138.png

Downloads & links

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Map

FileDownload / File: emd_10138.map.gz / Format: CCP4 / Size: 11.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSegment of helical membrane tube with longitudinal ESCRT-III filaments with different binding modes formed from Snf7/Vps24/Vps2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.28 Å/pix.
x 120 pix.
= 513.6 Å		4.28 Å/pix.
x 160 pix.
= 684.8 Å		4.28 Å/pix.
x 160 pix.
= 684.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 4.28 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.6 / Movie #1: 1.6
Minimum - Maximum-6.9243755 - 4.1664543
Average (Standard dev.)-0.7235882 (±1.0166994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-79-79-59
Dimensions160160120
Spacing160160120
CellA: 684.80005 Å / B: 684.80005 Å / C: 513.60004 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.284.284.28
M x/y/z160160120
origin x/y/z0.0000.0000.000
length x/y/z684.800684.800513.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-79-79-59
NC/NR/NS160160120
D min/max/mean-6.9244.166-0.724

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Supplemental data

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Additional map: #1

Fileemd_10138_additional.map
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Additional map: #1

Fileemd_10138_additional_1.map
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Half map: #2

Fileemd_10138_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_10138_half_map_2.map
Projections & Slices
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Sample components

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Entire : Segment of helical membrane tube with longitudinal ESCRT-III fila...

EntireName: Segment of helical membrane tube with longitudinal ESCRT-III filaments with different binding modes formed from Snf7/Vps24/Vps2
Components
  • Complex: Segment of helical membrane tube with longitudinal ESCRT-III filaments with different binding modes formed from Snf7/Vps24/Vps2

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Supramolecule #1: Segment of helical membrane tube with longitudinal ESCRT-III fila...

SupramoleculeName: Segment of helical membrane tube with longitudinal ESCRT-III filaments with different binding modes formed from Snf7/Vps24/Vps2
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
Processingsubtomogram averaging
Aggregation statefilament

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 120.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 31.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Dynamo (ver. 1.401) / Number subtomograms used: 17
ExtractionNumber tomograms: 17 / Number images used: 8150 / Software - Name: Dynamo (ver. 1.401)
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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