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- EMDB-10720: Cryo-tomography of ESCRT III CHMP4B/CHMP2B filaments bound to lip... -

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Basic information

Entry
Database: EMDB / ID: EMD-10720
TitleCryo-tomography of ESCRT III CHMP4B/CHMP2B filaments bound to liposomes
Map dataexample cryo-tomogram of ESCRT III bound to liposomes
Sample
  • Complex: CHMP4B, CHMP2B, lipids
    • Protein or peptide: CHMP4B
    • Protein or peptide: CHMP2B
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM
AuthorsBertin A / de Franceschi N / de la Mora E / Maity S / Miguet N / di Cicco A / Roos W / Mangenot S / Weissenhorn W / Bassereau P
Funding support France, 1 items
OrganizationGrant numberCountry
French National Research AgencyANR-14CE09-0003-01 France
CitationJournal: Nat Commun / Year: 2020
Title: Human ESCRT-III polymers assemble on positively curved membranes and induce helical membrane tube formation.
Authors: Aurélie Bertin / Nicola de Franceschi / Eugenio de la Mora / Sourav Maity / Maryam Alqabandi / Nolwen Miguet / Aurélie di Cicco / Wouter H Roos / Stéphanie Mangenot / Winfried Weissenhorn ...Authors: Aurélie Bertin / Nicola de Franceschi / Eugenio de la Mora / Sourav Maity / Maryam Alqabandi / Nolwen Miguet / Aurélie di Cicco / Wouter H Roos / Stéphanie Mangenot / Winfried Weissenhorn / Patricia Bassereau /
Abstract: Endosomal sorting complexes for transport-III (ESCRT-III) assemble in vivo onto membranes with negative Gaussian curvature. How membrane shape influences ESCRT-III polymerization and how ESCRT-III ...Endosomal sorting complexes for transport-III (ESCRT-III) assemble in vivo onto membranes with negative Gaussian curvature. How membrane shape influences ESCRT-III polymerization and how ESCRT-III shapes membranes is yet unclear. Human core ESCRT-III proteins, CHMP4B, CHMP2A, CHMP2B and CHMP3 are used to address this issue in vitro by combining membrane nanotube pulling experiments, cryo-electron tomography and AFM. We show that CHMP4B filaments preferentially bind to flat membranes or to tubes with positive mean curvature. Both CHMP2B and CHMP2A/CHMP3 assemble on positively curved membrane tubes. Combinations of CHMP4B/CHMP2B and CHMP4B/CHMP2A/CHMP3 are recruited to the neck of pulled membrane tubes and reshape vesicles into helical "corkscrew-like" membrane tubes. Sub-tomogram averaging reveals that the ESCRT-III filaments assemble parallel and locally perpendicular to the tube axis, highlighting the mechanical stresses imposed by ESCRT-III. Our results underline the versatile membrane remodeling activity of ESCRT-III that may be a general feature required for cellular membrane remodeling processes.
History
DepositionMar 2, 2020-
Header (metadata) releaseJun 10, 2020-
Map releaseJun 10, 2020-
UpdateJun 10, 2020-
Current statusJun 10, 2020Processing site: PDBe / Status: Released

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Structure visualization

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

emd_10720.png

Downloads & links

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Map

FileDownload / File: emd_10720.map.gz / Format: CCP4 / Size: 613.4 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Annotationexample cryo-tomogram of ESCRT III bound to liposomes
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.3 Å/pix.
x 361 pix.
= 1913.3 Å		5.3 Å/pix.
x 928 pix.
= 4918.4 Å		5.3 Å/pix.
x 960 pix.
= 5088. 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: 5.3 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-94 - 86
Average (Standard dev.)0.55204535 (±6.837252)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin18017-16
Dimensions928960361
Spacing960928361
CellA: 5088.0 Å / B: 4918.4004 Å / C: 1913.3 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z5.35.35.3
M x/y/z960928361
origin x/y/z0.0000.0000.000
length x/y/z5088.0004918.4001913.300
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS17180-16
NC/NR/NS960928361
D min/max/mean-94.00086.0000.552

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Supplemental data

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Additional map: sub-tomogram averaging: doublets of CHMP4/CHMP2B filaments bound to...

Fileemd_10720_additional_1.map
Annotationsub-tomogram averaging: doublets of CHMP4/CHMP2B filaments bound to tubes
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: sub-tomogram averaging: network of CHMP4/CHMP2B filaments bound to...

Fileemd_10720_additional_2.map
Annotationsub-tomogram averaging: network of CHMP4/CHMP2B filaments bound to tubes
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: sub-tomogram averaging: single CHMP4/CHMP2B filaments bound to tubes

Fileemd_10720_additional_3.map
Annotationsub-tomogram averaging: single CHMP4/CHMP2B filaments bound to tubes
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CHMP4B, CHMP2B, lipids

EntireName: CHMP4B, CHMP2B, lipids
Components
  • Complex: CHMP4B, CHMP2B, lipids
    • Protein or peptide: CHMP4B
    • Protein or peptide: CHMP2B

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Supramolecule #1: CHMP4B, CHMP2B, lipids

SupramoleculeName: CHMP4B, CHMP2B, lipids / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: CHMP4B

MacromoleculeName: CHMP4B / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
SequenceString: MSVFGKLFGA GGGKAGKGG P TPQEAIQR LR DTEEMLS KKQ EFLEKK IEQE LTAAK KHGTK NKRA ALQALK RKK RYEKQLA QI DGTLSTIE F QREALENAN TNTEVLKNMG YAAKAMKAA H DNMDIDKV DE LMQDIAD QQE LAEEIS TAIS KPVGF ...String:
MSVFGKLFGA GGGKAGKGG P TPQEAIQR LR DTEEMLS KKQ EFLEKK IEQE LTAAK KHGTK NKRA ALQALK RKK RYEKQLA QI DGTLSTIE F QREALENAN TNTEVLKNMG YAAKAMKAA H DNMDIDKV DE LMQDIAD QQE LAEEIS TAIS KPVGF GEEFD EDEL MAELEE LEQ EELDKNL LE ISGPETVP L PNVPSIALP SKPAKKKEEE DDDMKELEN W AGSM

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Macromolecule #2: CHMP2B

MacromoleculeName: CHMP2B / type: protein_or_peptide / ID: 2 / Enantiomer: DEXTRO
SequenceString: MASLFKKKTV DDVIKEQNR E LRGTQRAI IR DRAALEK QEK QLELEI KKMA KIGNK EACKV LAKQ LVHLRK QKT RTFAVSS KV TSMSTQTK V MNSQMKMAG AMSTTAKTMQ AVNKKMDPQ K TLQTMQNF QK ENMKMEM TEE MINDTL DDIF DGSDD ...String:
MASLFKKKTV DDVIKEQNR E LRGTQRAI IR DRAALEK QEK QLELEI KKMA KIGNK EACKV LAKQ LVHLRK QKT RTFAVSS KV TSMSTQTK V MNSQMKMAG AMSTTAKTMQ AVNKKMDPQ K TLQTMQNF QK ENMKMEM TEE MINDTL DDIF DGSDD EEESQ DIVN QVLDEI GIE ISGKMAK AP SAARSLPS A STSKATISD EEIERQLKAL GVD

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation state2D array

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE
Detailsprotein filaments bound to liposomes
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Sigma Aldrich / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 5.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 41

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