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- EMDB-14631: Membrane-bound CHMP2A-CHMP3 filament (410 Angstrom diameter) -

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Basic information

Entry
Database: EMDB / ID: EMD-14631
TitleMembrane-bound CHMP2A-CHMP3 filament (410 Angstrom diameter)
Map dataMembrane-bound CHMP2A-CHMP3 filament (410 Angstrom diameter)
Sample
  • Complex: Membrane-bound CHMP2A-CHMP3 filament (410 Angstrom Diameter) cryo-EM map
    • Protein or peptide: Charged multivesicular body protein 2a
    • Protein or peptide: Charged multivesicular body protein 3
Function / homology
Function and homology information


negative regulation of centriole elongation / regulation of endosome size / membrane invagination / : / amphisome membrane / multivesicular body-lysosome fusion / suppression of viral release by host / vesicle fusion with vacuole / ESCRT III complex disassembly / late endosome to lysosome transport ...negative regulation of centriole elongation / regulation of endosome size / membrane invagination / : / amphisome membrane / multivesicular body-lysosome fusion / suppression of viral release by host / vesicle fusion with vacuole / ESCRT III complex disassembly / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / endosome transport via multivesicular body sorting pathway / regulation of centrosome duplication / Sealing of the nuclear envelope (NE) by ESCRT-III / nuclear membrane reassembly / midbody abscission / multivesicular body sorting pathway / membrane coat / membrane fission / plasma membrane repair / phosphatidylcholine binding / late endosome to vacuole transport / multivesicular body membrane / positive regulation of exosomal secretion / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / exit from mitosis / multivesicular body assembly / regulation of mitotic spindle assembly / Translation of Replicase and Assembly of the Replication Transcription Complex / nucleus organization / Lysosome Vesicle Biogenesis / regulation of early endosome to late endosome transport / Macroautophagy / mitotic metaphase chromosome alignment / molecular function inhibitor activity / ubiquitin-specific protease binding / viral budding via host ESCRT complex / positive regulation of cytokinesis / autophagosome maturation / autophagosome membrane / protein polymerization / viral release from host cell / Pyroptosis / nuclear pore / Endosomal Sorting Complex Required For Transport (ESCRT) / phosphatidylinositol-4,5-bisphosphate binding / multivesicular body / viral budding from plasma membrane / HCMV Late Events / macroautophagy / Late endosomal microautophagy / establishment of protein localization / protein homooligomerization / Budding and maturation of HIV virion / kinetochore / autophagy / protein transport / late endosome / nuclear envelope / Translation of Replicase and Assembly of the Replication Transcription Complex / midbody / cytoplasmic vesicle / early endosome / lysosomal membrane / protein domain specific binding / apoptotic process / extracellular exosome / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Charged multivesicular body protein 2a / Charged multivesicular body protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsAzad K / Desfosses A / Effantin G / Schoehn G / Weissenhorn W
Funding support France, 3 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-14-CE09-0003-01 France
Agence Nationale de la Recherche (ANR)ANR-19-CE11-0002-02 France
Agence Nationale de la Recherche (ANR)ANR-17-EURE-0003 France
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: Structural basis of CHMP2A-CHMP3 ESCRT-III polymer assembly and membrane cleavage.
Authors: Kimi Azad / Delphine Guilligay / Cecile Boscheron / Sourav Maity / Nicola De Franceschi / Guidenn Sulbaran / Gregory Effantin / Haiyan Wang / Jean-Philippe Kleman / Patricia Bassereau / Guy ...Authors: Kimi Azad / Delphine Guilligay / Cecile Boscheron / Sourav Maity / Nicola De Franceschi / Guidenn Sulbaran / Gregory Effantin / Haiyan Wang / Jean-Philippe Kleman / Patricia Bassereau / Guy Schoehn / Wouter H Roos / Ambroise Desfosses / Winfried Weissenhorn /
Abstract: The endosomal sorting complex required for transport (ESCRT) is a highly conserved protein machinery that drives a divers set of physiological and pathological membrane remodeling processes. However, ...The endosomal sorting complex required for transport (ESCRT) is a highly conserved protein machinery that drives a divers set of physiological and pathological membrane remodeling processes. However, the structural basis of ESCRT-III polymers stabilizing, constricting and cleaving negatively curved membranes is yet unknown. Here we present cryo-EM structures of membrane-coated CHMP2A-CHMP3 filaments from Homo sapiens of two different diameters at 3.3 and 3.6 Å resolution. The structures reveal helical filaments assembled by CHMP2A-CHMP3 heterodimers in the open ESCRT-III conformation, which generates a partially positive charged membrane interaction surface, positions short N-terminal motifs for membrane interaction and the C-terminal VPS4 target sequence toward the tube interior. Inter-filament interactions are electrostatic, which may facilitate filament sliding upon VPS4-mediated polymer remodeling. Fluorescence microscopy as well as high-speed atomic force microscopy imaging corroborate that VPS4 can constrict and cleave CHMP2A-CHMP3 membrane tubes. We therefore conclude that CHMP2A-CHMP3-VPS4 act as a minimal membrane fission machinery.
History
DepositionMar 28, 2022-
Header (metadata) releaseJan 18, 2023-
Map releaseJan 18, 2023-
UpdateFeb 1, 2023-
Current statusFeb 1, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14631.png

Downloads & links

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Map

FileDownload / File: emd_14631.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMembrane-bound CHMP2A-CHMP3 filament (410 Angstrom diameter)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 768 pix.
= 807.936 Å		1.05 Å/pix.
x 768 pix.
= 807.936 Å		1.05 Å/pix.
x 768 pix.
= 807.936 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.052 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.019424388 - 0.02994373
Average (Standard dev.)6.6687094e-06 (±0.00054848264)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions768768768
Spacing768768768
CellA=B=C: 807.93604 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Membrane-bound CHMP2A-CHMP3 filament (410 Angstrom diameter) half map...

Fileemd_14631_half_map_1.map
AnnotationMembrane-bound CHMP2A-CHMP3 filament (410 Angstrom diameter) half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Membrane-bound CHMP2A-CHMP3 filament (410 Angstrom diameter) half map...

Fileemd_14631_half_map_2.map
AnnotationMembrane-bound CHMP2A-CHMP3 filament (410 Angstrom diameter) half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Membrane-bound CHMP2A-CHMP3 filament (410 Angstrom Diameter) cryo...

EntireName: Membrane-bound CHMP2A-CHMP3 filament (410 Angstrom Diameter) cryo-EM map
Components
  • Complex: Membrane-bound CHMP2A-CHMP3 filament (410 Angstrom Diameter) cryo-EM map
    • Protein or peptide: Charged multivesicular body protein 2a
    • Protein or peptide: Charged multivesicular body protein 3

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Supramolecule #1: Membrane-bound CHMP2A-CHMP3 filament (410 Angstrom Diameter) cryo...

SupramoleculeName: Membrane-bound CHMP2A-CHMP3 filament (410 Angstrom Diameter) cryo-EM map
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Charged multivesicular body protein 2a

MacromoleculeName: Charged multivesicular body protein 2a / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.305488 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
RKTPEELLRQ NQRALNRAMR ELDRERQKLE TQEKKIIADI KKMAKQGQMD AVRIMAKDLV RTRRYVRKFV LMRANIQAVS LKIQTLKSN NSMAQAMKGV TKAMGTMNRQ LKLPQIQKIM MEFERQAEIM DMKEEMMNDA IDDAMGDE

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Macromolecule #2: Charged multivesicular body protein 3

MacromoleculeName: Charged multivesicular body protein 3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.429684 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
PPKELVNEWS LKIRKEMRVV DRQIRDIQRE EEKVKRSVKD AAKKGQKDVC IVLAKEMIRS RKAVSKLYAS KAHMNSVLMG MKNQLAVLR VAGSLQKSTE VMKAMQSLVK IPEIQATMRE LSKEMMKAGI IEEMLEDTFE SMDDQEEMEE EAEMEIDRIL

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
25.0 mMC4H11NO3Tris
25.0 mMNaClSodium chlorideSodium Chloride
1.0 mMC2H6OSBeta-mercaptoethanol2-Mercaptoethanol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV

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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 / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 5028 / Average exposure time: 5.0 sec. / Average electron dose: 24.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Segment selectionNumber selected: 89122
Final angle assignmentType: NOT APPLICABLE
Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 1.44 Å
Applied symmetry - Helical parameters - Δ&Phi: 57.049 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 11396
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6tz4

RefinementSpace: REAL
Output model

PDB-7zch:
CHMP2A-CHMP3 heterodimer (410 Angstrom diameter)

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