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Open data
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Basic information
Entry | Database: PDB / ID: 9hzv | ||||||||||||||||||
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Title | 250 A SynPspA rod after incubation with EPL | ||||||||||||||||||
![]() | Chloroplast membrane-associated 30 kD protein | ||||||||||||||||||
![]() | LIPID BINDING PROTEIN / Nucleotide binding / Helical assembly / ESCRT-III fold / Membrane remodeling | ||||||||||||||||||
Function / homology | PspA/IM30 / PspA/IM30 family / Chloroplast membrane-associated 30 kD protein![]() | ||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 6.1 Å | ||||||||||||||||||
![]() | Hudina, E. / Junglas, B. / Sachse, C. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: The bacterial ESCRT-III PspA rods thin lipid tubules and increase membrane curvature through helix α0 interactions. Authors: Esther Hudina / Stephan Schott-Verdugo / Benedikt Junglas / Mirka Kutzner / Ilona Ritter / Nadja Hellmann / Dirk Schneider / Holger Gohlke / Carsten Sachse / ![]() Abstract: The phage shock protein A (PspA), a bacterial member of the endosomal sorting complexes required for transport (ESCRT)-III superfamily, forms rod-shaped helical assemblies that internalize membrane ...The phage shock protein A (PspA), a bacterial member of the endosomal sorting complexes required for transport (ESCRT)-III superfamily, forms rod-shaped helical assemblies that internalize membrane tubules. The N-terminal helix α0 of PspA (and other ESCRT-III members) has been suggested to act as a membrane anchor; the detailed mechanism, however, of how it binds to membranes and eventually triggers membrane fusion and/or fission events remains unclear. By solving a total of 15 cryoelectron microscopy (cryo-EM) structures of PspA and a truncation lacking the N-terminal helix α0 in the presence of polar lipid membranes, we show in molecular detail how PspA interacts with and remodels membranes: Binding of the N-terminal helix α0 in the outer tubular membrane leaflet induces membrane curvature, supporting membrane tubulation by PspA. Detailed molecular dynamics simulations and free energy computations of interactions between the helix α0 and negatively charged membranes suggest a compensating mechanism between helix-membrane interactions and the energy contributions required for membrane bending. The energetic considerations are in line with the membrane structures observed in the cryo-EM images of tubulated membrane vesicles, fragmented vesicles inside tapered PspA rods, and shedded vesicles emerging at the thinner PspA rod ends. Our results provide insights into the molecular determinants and a potential mechanism of vesicular membrane remodeling mediated by a member of the ESCRT-III superfamily. | ||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 3.8 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 277.3 KB | Display | |
Data in CIF | ![]() | 382.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 15503 ![]() 52535MC ![]() 9hzmC ![]() 9hznC ![]() 9hzoC ![]() 9hzpC ![]() 9hzqC ![]() 9hzrC ![]() 9hzsC ![]() 9hztC ![]() 9hzuC ![]() 9hzwC ![]() 9hzxC ![]() 9hzyC ![]() 9hzzC ![]() 9i00C ![]() 9i01C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 28097.758 Da / Num. of mol.: 60 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Details (production host): Based on pET50b(+) with deletion of NusA tag Production host: ![]() ![]() Has protein modification | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
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Sample preparation
Component | Name: Helical assembly of SynPspA after incubation with EPL / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 1.7 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 44 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
EM software | Name: PHENIX / Version: 1.21.2_5419 / Category: model refinement |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Helical symmerty | Angular rotation/subunit: -83.6 ° / Axial rise/subunit: 2.12 Å / Axial symmetry: C1 |
3D reconstruction | Resolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34131 / Symmetry type: HELICAL |
Refinement | Cross valid method: NONE |