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- EMDB-11482: C16 symmetry: Bacterial Vipp1 and PspA are members of the ancient... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11482 | |||||||||
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Title | C16 symmetry: Bacterial Vipp1 and PspA are members of the ancient ESCRT-III membrane-remodeling superfamily. | |||||||||
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Function / homology | phage shock / PspA/IM30 / PspA/IM30 family / lipid binding / plasma membrane / cytosol / Membrane-associated protein Vipp1![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.4 Å | |||||||||
![]() | Liu J / Tassinari M / Souza DP / Naskar S / Noel JK / Bohuszewicz O / Buck M / Williams TA / Baum B / Low HH | |||||||||
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. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 20.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.1 KB 10.1 KB | Display Display | ![]() |
Images | ![]() | 36.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zw6MC ![]() 6zvrC ![]() 6zvsC ![]() 6zvtC ![]() 6zw4C ![]() 6zw5C ![]() 6zw7C C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : vipp1 c16 ring
Entire | Name: vipp1 c16 ring |
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Components |
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-Supramolecule #1: vipp1 c16 ring
Supramolecule | Name: vipp1 c16 ring / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #1: vipp1
Macromolecule | Name: vipp1 / type: protein_or_peptide / ID: 1 / Number of copies: 112 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 28.745461 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGLFDRIKRV VSSNLNDLVN KAEDPEKMLE QAILEMQEDL VQLRQGVAQA IAAQKRSEKQ YNDAQNEINK WQRNAQLALQ KGDENLARQ ALERKKTYTD TSAALKASLD TQSTQVETLK RNLIQLESKI SEAKTKKEML KARITTAKAQ EQLQGMVRGM N TSSAMSAF ...String: MGLFDRIKRV VSSNLNDLVN KAEDPEKMLE QAILEMQEDL VQLRQGVAQA IAAQKRSEKQ YNDAQNEINK WQRNAQLALQ KGDENLARQ ALERKKTYTD TSAALKASLD TQSTQVETLK RNLIQLESKI SEAKTKKEML KARITTAKAQ EQLQGMVRGM N TSSAMSAF ERMEEKVLMQ ESRAQALGEL AGADLETQFA QLEGGSDVDD ELAALKAQML PPATPVTQAQ LPPQQETTPA KS NEVVDAE LDSLRKQLDQ L |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8.4 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 7.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 7017 |
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Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |