+Open data
-Basic information
Entry | Database: PDB / ID: 7zch | ||||||||||||
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Title | CHMP2A-CHMP3 heterodimer (410 Angstrom diameter) | ||||||||||||
Components |
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Keywords | CYTOSOLIC PROTEIN / Cryo Electron Microscopy / Helical Reconstruction / Membrane-bound CHMP2A-CHMP3 filament / Negative-curvature membrane | ||||||||||||
Function / homology | : / : Function and homology information | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||
Authors | Azad, K. / Desfosses, A. / Effantin, G. / Schoehn, G. / Weissenhorn, W. | ||||||||||||
Funding support | France, 3items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zch.cif.gz | 65.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zch.ent.gz | 47.5 KB | Display | PDB format |
PDBx/mmJSON format | 7zch.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zch_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7zch_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7zch_validation.xml.gz | 44.5 KB | Display | |
Data in CIF | 7zch_validation.cif.gz | 62.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/7zch ftp://data.pdbj.org/pub/pdb/validation_reports/zc/7zch | HTTPS FTP |
-Related structure data
Related structure data | 14631MC 7zcgC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 17305.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CHMP2A, BC2, CHMP2 / Plasmid: pMAL-c5X / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: O43633 |
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#2: Protein | Mass: 18429.684 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CHMP3, CGI149, NEDF, VPS24, CGI-149 / Plasmid: pProEX-HTb / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21Gold (DE3) / References: UniProt: Q9Y3E7 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Membrane-bound CHMP2A-CHMP3 filament (410 Angstrom Diameter) cryo-EM map Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 5 sec. / Electron dose: 24 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 5028 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 25 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 57.049 ° / Axial rise/subunit: 1.44 Å / Axial symmetry: C1 | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 89122 | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11396 / Num. of class averages: 1 / Symmetry type: HELICAL | ||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6TZ4 Accession code: 6TZ4 / Source name: PDB / Type: experimental model |