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- PDB-6zw7: C17 symmetry: Bacterial Vipp1 and PspA are members of the ancient... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zw7 | ||||||
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Title | C17 symmetry: Bacterial Vipp1 and PspA are members of the ancient ESCRT-III membrane-remodeling superfamily. | ||||||
![]() | vipp1 | ||||||
![]() | LIPID BINDING PROTEIN / membrane remodelling | ||||||
Function / homology | phage shock / PspA/IM30 / PspA/IM30 family / lipid binding / plasma membrane / cytosol / Membrane-associated protein Vipp1![]() | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.4 Å | ||||||
![]() | Liu, J. / Tassinari, M. / Souza, D.P. / Naskar, S. / Noel, J.K. / Bohuszewicz, O. / Buck, M. / Williams, T.A. / Baum, B. / Low, H.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Bacterial Vipp1 and PspA are members of the ancient ESCRT-III membrane-remodeling superfamily. Authors: Jiwei Liu / Matteo Tassinari / Diorge P Souza / Souvik Naskar / Jeffrey K Noel / Olga Bohuszewicz / Martin Buck / Tom A Williams / Buzz Baum / Harry H Low / ![]() ![]() Abstract: Membrane remodeling and repair are essential for all cells. Proteins that perform these functions include Vipp1/IM30 in photosynthetic plastids, PspA in bacteria, and ESCRT-III in eukaryotes. Here, ...Membrane remodeling and repair are essential for all cells. Proteins that perform these functions include Vipp1/IM30 in photosynthetic plastids, PspA in bacteria, and ESCRT-III in eukaryotes. Here, using a combination of evolutionary and structural analyses, we show that these protein families are homologous and share a common ancient evolutionary origin that likely predates the last universal common ancestor. This homology is evident in cryo-electron microscopy structures of Vipp1 rings from the cyanobacterium Nostoc punctiforme presented over a range of symmetries. Each ring is assembled from rungs that stack and progressively tilt to form dome-shaped curvature. Assembly is facilitated by hinges in the Vipp1 monomer, similar to those in ESCRT-III proteins, which allow the formation of flexible polymers. Rings have an inner lumen that is able to bind and deform membranes. Collectively, these data suggest conserved mechanistic principles that underlie Vipp1, PspA, and ESCRT-III-dependent membrane remodeling across all domains of life. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 3 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 11483MC ![]() 6zvrC ![]() 6zvsC ![]() 6zvtC ![]() 6zw4C ![]() 6zw5C ![]() 6zw6C C: citing same article ( M: map data used to model this data |
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Similar structure data |
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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: 28745.461 Da / Num. of mol.: 119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: vipp1 c17 ring / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 8.4 |
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: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 1.5 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
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EM software | Name: RELION / Category: 3D reconstruction | ||||||||||||||||||||||||
CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 9.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4055 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 851.99 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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