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- EMDB-19863: 250A Vipp1 dL10Ala helical tubes in the presence of EPL -

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Basic information

Entry
Database: EMDB / ID: EMD-19863
Title250A Vipp1 dL10Ala helical tubes in the presence of EPL
Map data
Sample
  • Complex: Vipp1 dL10Ala
    • Protein or peptide: Membrane-associated protein Vipp1
Keywordsmembrane remodeling / membrane tubulation / LIPID BINDING PROTEIN
Function / homologyPspA/IM30 / PspA/IM30 family / plasma membrane / Membrane-associated protein Vipp1
Function and homology information
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 5.5 Å
AuthorsJunglas B / Sachse C
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SA 1882/6-1 Germany
German Research Foundation (DFG)SCHN 690/16-1 Germany
Citation
Journal: Nat Struct Mol Biol / Year: 2025
Title: Structural basis for Vipp1 membrane binding: from loose coats and carpets to ring and rod assemblies.
Authors: Benedikt Junglas / David Kartte / Mirka Kutzner / Nadja Hellmann / Ilona Ritter / Dirk Schneider / Carsten Sachse /
Abstract: Vesicle-inducing protein in plastids 1 (Vipp1) is critical for thylakoid membrane biogenesis and maintenance. Although Vipp1 has recently been identified as a member of the endosomal sorting ...Vesicle-inducing protein in plastids 1 (Vipp1) is critical for thylakoid membrane biogenesis and maintenance. Although Vipp1 has recently been identified as a member of the endosomal sorting complexes required for transport III superfamily, it is still unknown how Vipp1 remodels membranes. Here, we present cryo-electron microscopy structures of Synechocystis Vipp1 interacting with membranes: seven structures of helical and stacked-ring assemblies at 5-7-Å resolution engulfing membranes and three carpet structures covering lipid vesicles at ~20-Å resolution using subtomogram averaging. By analyzing ten structures of N-terminally truncated Vipp1, we show that helix α0 is essential for membrane tubulation and forms the membrane-anchoring domain of Vipp1. Lastly, using a conformation-restrained Vipp1 mutant, we reduced the structural plasticity of Vipp1 and determined two structures of Vipp1 at 3.0-Å resolution, resolving the molecular details of membrane-anchoring and intersubunit contacts of helix α0. Our data reveal membrane curvature-dependent structural transitions from carpets to rings and rods, some of which are capable of inducing and/or stabilizing high local membrane curvature triggering membrane fusion.
#1: Journal: Biorxiv / Year: 2024
Title: Structural basis for Vipp1 membrane binding: From loose coats and carpets to ring and rod assemblies
Authors: Junglas B / Kartte D / Kutzner M / Hellmann N / Ritter I / Schneider D / Sachse C
History
DepositionMar 15, 2024-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19863.png

Downloads & links

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Map

FileDownload / File: emd_19863.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 500 pix.
= 680. Å		1.36 Å/pix.
x 500 pix.
= 680. Å		1.36 Å/pix.
x 500 pix.
= 680. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.768
Minimum - Maximum-0.96840036 - 1.9774145
Average (Standard dev.)0.012176339 (±0.08828433)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 680.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_19863_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_19863_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Vipp1 dL10Ala

EntireName: Vipp1 dL10Ala
Components
  • Complex: Vipp1 dL10Ala
    • Protein or peptide: Membrane-associated protein Vipp1

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Supramolecule #1: Vipp1 dL10Ala

SupramoleculeName: Vipp1 dL10Ala / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)

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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: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 29.857445 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGLFDRLGRV VRANLNDLVS KAEDPEKVLE QAVIDMQEDL VQLRQAVART IAEEKRTEQR LNQDTQEAKK WEDRAKLALT NGEENLARE ALARKKSLTD TAAAYQTQLA QQRTMSENLR RNLAALEAKI SEAKTKKNML QARAKAAKAN AELQQTLAAA A AAAAAAAF ...String:
MGLFDRLGRV VRANLNDLVS KAEDPEKVLE QAVIDMQEDL VQLRQAVART IAEEKRTEQR LNQDTQEAKK WEDRAKLALT NGEENLARE ALARKKSLTD TAAAYQTQLA QQRTMSENLR RNLAALEAKI SEAKTKKNML QARAKAAKAN AELQQTLAAA A AAAAAAAF ERMENKVLDM EATSQAAGEL AGFGIENQFA QLEASSGVED ELAALKASMA GGALPGTSAA TPQLEAAPVD SS VPANNAS QDDAVIDQEL DDLRRRLNNL AALEVLFQGP

UniProtKB: Membrane-associated protein Vipp1

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 8
Sugar embeddingMaterial: vitreous ice
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.53 Å
Applied symmetry - Helical parameters - Δ&Phi: 62.40 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 156661
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7o3w

Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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