+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14631 | ||||||||||||
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Title | Membrane-bound CHMP2A-CHMP3 filament (410 Angstrom diameter) | ||||||||||||
Map data | Membrane-bound CHMP2A-CHMP3 filament (410 Angstrom diameter) | ||||||||||||
Sample |
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Keywords | Cryo Electron Microscopy / Helical Reconstruction / Membrane-bound CHMP2A-CHMP3 filament / Negative-curvature membrane / CYTOSOLIC PROTEIN | ||||||||||||
Function / homology | Function and homology information negative regulation of centriole elongation / regulation of endosome size / membrane invagination / amphisome membrane / multivesicular body-lysosome fusion / vesicle fusion with vacuole / suppression of viral release by host / ESCRT III complex disassembly / late endosome to lysosome transport / ESCRT III complex ...negative regulation of centriole elongation / regulation of endosome size / membrane invagination / amphisome membrane / multivesicular body-lysosome fusion / vesicle fusion with vacuole / suppression of viral release by host / 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 / nuclear membrane reassembly / Sealing of the nuclear envelope (NE) by ESCRT-III / midbody abscission / multivesicular body sorting pathway / membrane coat / membrane fission / plasma membrane repair / late endosome to vacuole transport / phosphatidylcholine binding / multivesicular body membrane / positive regulation of exosomal secretion / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / regulation of mitotic spindle assembly / Translation of Replicase and Assembly of the Replication Transcription Complex / exit from mitosis / Lysosome Vesicle Biogenesis / regulation of early endosome to late endosome transport / mitotic metaphase chromosome alignment / Macroautophagy / molecular function inhibitor activity / nucleus organization / ubiquitin-specific protease binding / viral budding via host ESCRT complex / positive regulation of cytokinesis / autophagosome membrane / autophagosome maturation / viral release from host cell / protein polymerization / 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 / Budding and maturation of HIV virion / protein homooligomerization / kinetochore / autophagy / protein transport / late endosome / nuclear envelope / Translation of Replicase and Assembly of the Replication Transcription Complex / midbody / cytoplasmic vesicle / early endosome / protein domain specific binding / lysosomal membrane / apoptotic process / chromatin / extracellular exosome / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||
Authors | Azad K / Desfosses A / Effantin G / Schoehn G / Weissenhorn W | ||||||||||||
Funding support | France, 3 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14631.map.gz | 91 MB | EMDB map data format | |
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Header (meta data) | emd-14631-v30.xml emd-14631.xml | 18.7 KB 18.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14631_fsc.xml | 27 KB | Display | FSC data file |
Images | emd_14631.png | 163.5 KB | ||
Filedesc metadata | emd-14631.cif.gz | 6.2 KB | ||
Others | emd_14631_half_map_1.map.gz emd_14631_half_map_2.map.gz | 1.4 GB 1.4 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14631 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14631 | HTTPS FTP |
-Validation report
Summary document | emd_14631_validation.pdf.gz | 859.5 KB | Display | EMDB validaton report |
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Full document | emd_14631_full_validation.pdf.gz | 859 KB | Display | |
Data in XML | emd_14631_validation.xml.gz | 35.1 KB | Display | |
Data in CIF | emd_14631_validation.cif.gz | 47.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14631 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14631 | HTTPS FTP |
-Related structure data
Related structure data | 7zchMC 7zcgC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_14631.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Membrane-bound CHMP2A-CHMP3 filament (410 Angstrom diameter) | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.052 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Membrane-bound CHMP2A-CHMP3 filament (410 Angstrom diameter) half map...
File | emd_14631_half_map_1.map | ||||||||||||
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Annotation | Membrane-bound CHMP2A-CHMP3 filament (410 Angstrom diameter) half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Membrane-bound CHMP2A-CHMP3 filament (410 Angstrom diameter) half map...
File | emd_14631_half_map_2.map | ||||||||||||
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Annotation | Membrane-bound CHMP2A-CHMP3 filament (410 Angstrom diameter) half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Membrane-bound CHMP2A-CHMP3 filament (410 Angstrom Diameter) cryo...
Entire | Name: Membrane-bound CHMP2A-CHMP3 filament (410 Angstrom Diameter) cryo-EM map |
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Components |
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-Supramolecule #1: Membrane-bound CHMP2A-CHMP3 filament (410 Angstrom Diameter) cryo...
Supramolecule | Name: Membrane-bound CHMP2A-CHMP3 filament (410 Angstrom Diameter) cryo-EM map type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Charged multivesicular body protein 2a
Macromolecule | Name: Charged multivesicular body protein 2a / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 17.305488 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: RKTPEELLRQ NQRALNRAMR ELDRERQKLE TQEKKIIADI KKMAKQGQMD AVRIMAKDLV RTRRYVRKFV LMRANIQAVS LKIQTLKSN NSMAQAMKGV TKAMGTMNRQ LKLPQIQKIM MEFERQAEIM DMKEEMMNDA IDDAMGDE UniProtKB: Charged multivesicular body protein 2a |
-Macromolecule #2: Charged multivesicular body protein 3
Macromolecule | Name: Charged multivesicular body protein 3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 18.429684 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: PPKELVNEWS LKIRKEMRVV DRQIRDIQRE EEKVKRSVKD AAKKGQKDVC IVLAKEMIRS RKAVSKLYAS KAHMNSVLMG MKNQLAVLR VAGSLQKSTE VMKAMQSLVK IPEIQATMRE LSKEMMKAGI IEEMLEDTFE SMDDQEEMEE EAEMEIDRIL UniProtKB: Charged multivesicular body protein 3 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 1 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film 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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |