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- EMDB-18321: Cryo-EM structure of Vipp1-deltaH6_aa1-219 helical filament with ... -

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Basic information

Entry
Database: EMDB / ID: EMD-18321
TitleCryo-EM structure of Vipp1-deltaH6_aa1-219 helical filament with lattice 2 (Vipp1-deltaH6_L2)
Map dataPrimary sharpened map.
Sample
  • Complex: Vipp1-deltaH6_L2
    • Protein or peptide: Membrane-associated protein Vipp1
KeywordsVipp1/IM30/ESCRT-III / Membrane remodeling / Cryoelectron microscopy / Helical filament structure / 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)
Methodhelical reconstruction / cryo EM / Resolution: 3.78 Å
AuthorsNaskar S / Low HH
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust215553/Z/19/Z United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Mechanism for Vipp1 spiral formation, ring biogenesis, and membrane repair.
Authors: Souvik Naskar / Andrea Merino / Javier Espadas / Jayanti Singh / Aurelien Roux / Adai Colom / Harry H Low /
Abstract: The ESCRT-III-like protein Vipp1 couples filament polymerization with membrane remodeling. It assembles planar sheets as well as 3D rings and helical polymers, all implicated in mitigating plastid- ...The ESCRT-III-like protein Vipp1 couples filament polymerization with membrane remodeling. It assembles planar sheets as well as 3D rings and helical polymers, all implicated in mitigating plastid-associated membrane stress. The architecture of Vipp1 planar sheets and helical polymers remains unknown, as do the geometric changes required to transition between polymeric forms. Here we show how cyanobacterial Vipp1 assembles into morphologically-related sheets and spirals on membranes in vitro. The spirals converge to form a central ring similar to those described in membrane budding. Cryo-EM structures of helical filaments reveal a close geometric relationship between Vipp1 helical and planar lattices. Moreover, the helical structures reveal how filaments twist-a process required for Vipp1, and likely other ESCRT-III filaments, to transition between planar and 3D architectures. Overall, our results provide a molecular model for Vipp1 ring biogenesis and a mechanism for Vipp1 membrane stabilization and repair, with implications for other ESCRT-III systems.
History
DepositionAug 25, 2023-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18321.png

Downloads & links

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Map

FileDownload / File: emd_18321.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary sharpened map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.1 Å/pix.
x 450 pix.
= 495. Å		1.1 Å/pix.
x 450 pix.
= 495. Å		1.1 Å/pix.
x 450 pix.
= 495. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.3
Minimum - Maximum-19.276806000000001 - 27.704027
Average (Standard dev.)-0.000000000000225 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 495.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened and unmasked raw map from 3D auto-refinement.

Fileemd_18321_additional_1.map
AnnotationUnsharpened and unmasked raw map from 3D auto-refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unmasked raw half-map 1.

Fileemd_18321_half_map_1.map
AnnotationUnmasked raw half-map 1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unmasked raw half-map 2.

Fileemd_18321_half_map_2.map
AnnotationUnmasked raw half-map 2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Vipp1-deltaH6_L2

EntireName: Vipp1-deltaH6_L2
Components
  • Complex: Vipp1-deltaH6_L2
    • Protein or peptide: Membrane-associated protein Vipp1

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Supramolecule #1: Vipp1-deltaH6_L2

SupramoleculeName: Vipp1-deltaH6_L2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Nostoc punctiforme (bacteria) / Strain: ATCC 29133 / PCC 73102

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Macromolecule #1: Membrane-associated protein Vipp1

MacromoleculeName: Membrane-associated protein Vipp1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Nostoc punctiforme (bacteria) / Strain: ATCC 29133 / PCC 73102
Molecular weightTheoretical: 24.292504 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 ELAALKAQM

UniProtKB: Membrane-associated protein Vipp1

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration1.5 mg/mL
BufferpH: 8.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 50 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 3.0 sec. / 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 / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.75 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.15543 Å
Applied symmetry - Helical parameters - Δ&Phi: 68.507182 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.78 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number images used: 38361
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Overall B value: 189.95
Output model

PDB-8qbv:
Cryo-EM structure of Vipp1-deltaH6_aa1-219 helical filament with lattice 2 (Vipp1-deltaH6_L2)

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