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- EMDB-0321: cryotomogram of septins bound to vesicles -

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Basic information

Entry
Database: EMDB / ID: EMD-0321
Titlecryotomogram of septins bound to vesicles
Map data
Sample
  • Complex: septins bound to vesicles
    • Other: septin
Biological speciesSaccharomycetales (fungus)
Methodelectron tomography / cryo EM
AuthorsBertin A / Taveneau C
Funding support France, 1 items
OrganizationGrant numberCountry
French National Research AgencyANR-13-JSV8-0002-01 France
CitationJournal: Nat Commun / Year: 2019
Title: Membrane reshaping by micrometric curvature sensitive septin filaments.
Authors: Alexandre Beber / Cyntia Taveneau / Manuela Nania / Feng-Ching Tsai / Aurelie Di Cicco / Patricia Bassereau / Daniel Lévy / João T Cabral / Hervé Isambert / Stéphanie Mangenot / Aurélie Bertin /
Abstract: Septins are cytoskeletal filaments that assemble at the inner face of the plasma membrane. They are localized at constriction sites and impact membrane remodeling. We report in vitro tools to examine ...Septins are cytoskeletal filaments that assemble at the inner face of the plasma membrane. They are localized at constriction sites and impact membrane remodeling. We report in vitro tools to examine how yeast septins behave on curved and deformable membranes. Septins reshape the membranes of Giant Unilamellar Vesicles with the formation of periodic spikes, while flattening smaller vesicles. We show that membrane deformations are associated to preferential arrangement of septin filaments on specific curvatures. When binding to bilayers supported on custom-designed periodic wavy patterns displaying positive and negative micrometric radii of curvatures, septin filaments remain straight and perpendicular to the curvature of the convex parts, while bending negatively to follow concave geometries. Based on these results, we propose a theoretical model that describes the deformations and micrometric curvature sensitivity observed in vitro. The model captures the reorganizations of septin filaments throughout cytokinesis in vivo, providing mechanistic insights into cell division.
History
DepositionOct 25, 2018-
Header (metadata) releaseNov 20, 2019-
Map releaseNov 20, 2019-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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Movie viewer
Supplemental images

emd_0321.png

Downloads & links

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Map

FileDownload / File: emd_0321.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.52 Å/pix.
x 2048 pix.
= 17448.961 Å		8.52 Å/pix.
x 338 pix.
= 2879.76 Å		8.52 Å/pix.
x 1024 pix.
= 8724.48 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 8.52 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-6327 - 5542
Average (Standard dev.)219.24393 (±426.00385)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin16900
Dimensions33810242048
Spacing10243382048
CellA: 8724.48 Å / B: 2879.7603 Å / C: 17448.96 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z8.528.528.5200004882812
M x/y/z10243382048
origin x/y/z0.0000.0000.000
length x/y/z8724.4802879.76017448.961
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS01690
NC/NR/NS10243382048
D min/max/mean-6327.0005542.000219.244

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Supplemental data

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Sample components

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Entire : septins bound to vesicles

EntireName: septins bound to vesicles
Components
  • Complex: septins bound to vesicles
    • Other: septin

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Supramolecule #1: septins bound to vesicles

SupramoleculeName: septins bound to vesicles / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomycetales (fungus)
Recombinant expressionOrganism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)

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Macromolecule #1: septin

MacromoleculeName: septin / type: other / ID: 1 / Classification: other
Source (natural)Organism: Saccharomycetales (fungus)
SequenceString: ATGTCCGGAA TAATTGACGC ATCTTCTGCA TTAAGAAAAA GAAAGCATTT GAAAAGAGGT ATAACCTTCA CTGTGATGAT CGTGGGCCAG TCCGGATCTG GTAGATCGAC TTTTATAAAT ACTTTGTGCG GTCAGCAAGT TGTAGACACT TCGACGACAA TCTTGTTACC ...String:
ATGTCCGGAA TAATTGACGC ATCTTCTGCA TTAAGAAAAA GAAAGCATTT GAAAAGAGGT ATAACCTTCA CTGTGATGAT CGTGGGCCAG TCCGGATCTG GTAGATCGAC TTTTATAAAT ACTTTGTGCG GTCAGCAAGT TGTAGACACT TCGACGACAA TCTTGTTACC CACAGATACG TCCACAGAAA TAGACTTACA ATTGAGAGAG GAGACGGTCG AATTAGAAGA TGATGAAGGT GTCAAGATTC AACTTAATAT CATCGATACT CCGGGATTCG GTGATTCTCT CGACAATTCT CCATCTTTCG AAATCATTTC CGACTACATT CGCCACCAAT ATGATGAAAT CTTATTGGAA GAAAGTCGTG TGAGAAGAAA CCCAAGATTT AAGGACGGCA GAGTTCATTG TTGTCTTTAC TTAATCAACC CAACTGGCCA CGGTTTAAAA GAGATTGATG TGGAATTCAT CAGACAGTTG GGATCCTTAG TTAACATCAT CCCTGTGATC AGCAAATCAG ATTCCTTGAC AAGAGATGAA CTGAAACTGA ATAAAAAATT GATCATGGAG GATATCGACA GATGGAACTT GCCAATTTAT AATTTCCCTT TCGATGAAGA TGAAATATCA GACGAAGATT ACGAAACCAA TATGTACCTA CGTACACTTC TACCTTTTGC TATTATTGGA TCCAATGAAG TTTACGAAAT GGGCGGCGAT GTTGGGACAA TTCGTGGCAG AAAGTATCCA TGGGGCATAC TGGACGTGGA AGATTCATCG ATCTCTGATT TTGTTATCTT AAGGAATGCG TTATTGATCT CTCATTTACA TGACTTGAAA AACTACACAC ATGAGATATT ATATGAAAGA TATAGAACCG AGGCATTATC AGGTGAATCT GTCGCGGCAG AATCCATACG TCCAAATCTG ACAAAATTGA ATGGTTCGTC GTCATCGTCC ACCACAACAA GGAGAAACAC AAATCCCTTC AAGCAAAGTA ATAATATTAA TAACGATGTT CTCAACCCAG CATCCGATAT GCACGGGCAA AGCACTGGCG AAAATAACGA AACCTACATG ACACGTGAGG AGCAAATACG GTTAGAAGAA GAGCGACTAA AGGCATTTGA GGAGAGAGTT CAGCAAGAAC TGCTGTTGAA AAGACAAGAA CTGTTGCAAA GAGAAAAGGA ATTAAGAGAA ATTGAAGCCA GGTTGGAAAA AGAGGCGAAA ATCAAACAGG AAGAATGA
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statefilament

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE / Details: EMGP (Leica).
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: nanoprobes / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TECNAI 20
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 0.8 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD

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Image processing

Final reconstructionNumber images used: 73

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