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- EMDB-11470: C13 symmetry: Bacterial Vipp1 and PspA are members of the ancient... -

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Basic information

Entry
Database: EMDB / ID: EMD-11470
TitleC13 symmetry: Bacterial Vipp1 and PspA are members of the ancient ESCRT-III membrane-remodeling superfamily.
Map data
Sample
  • Complex: vipp1 c13 ring
    • Protein or peptide: Vipp1
Keywordsmembrane remodelling / LIPID BINDING PROTEIN
Function / homologyPspA/IM30 / PspA/IM30 family / lipid binding / plasma membrane / Membrane-associated protein Vipp1
Function and homology information
Biological speciesNostoc punctiforme (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.0 Å
AuthorsLiu JW / Tassinari M / Souza DP / Naskar S / Noel JK / Bohuszewicz O / Buck M / Williams TA / Baum B / Low HH
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Cell / Year: 2021
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
DepositionJul 27, 2020-
Header (metadata) releaseAug 4, 2021-
Map releaseAug 4, 2021-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0187
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0187
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6zvt
  • Surface level: 0.0187
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11470.png

Downloads & links

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Map

FileDownload / File: emd_11470.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 336 pix.
= 467.04 Å		1.39 Å/pix.
x 336 pix.
= 467.04 Å		1.39 Å/pix.
x 336 pix.
= 467.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.39 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0187 / Movie #1: 0.0187
Minimum - Maximum-0.009142844 - 0.054854285
Average (Standard dev.)0.000698973 (±0.003407305)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 467.04 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z336336336
origin x/y/z0.0000.0000.000
length x/y/z467.040467.040467.040
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS336336336
D min/max/mean-0.0090.0550.001

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Supplemental data

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Sample components

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Entire : vipp1 c13 ring

EntireName: vipp1 c13 ring
Components
  • Complex: vipp1 c13 ring
    • Protein or peptide: Vipp1

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Supramolecule #1: vipp1 c13 ring

SupramoleculeName: vipp1 c13 ring / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Nostoc punctiforme (bacteria)

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Macromolecule #1: Vipp1

MacromoleculeName: Vipp1 / type: protein_or_peptide / ID: 1 / Number of copies: 78 / Enantiomer: LEVO
Source (natural)Organism: Nostoc punctiforme (bacteria)
Molecular weightTheoretical: 28.745461 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

UniProtKB: Membrane-associated protein Vipp1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 6920
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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