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- EMDB-19904: C20 Vipp1 dL10Ala ring -

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Basic information

Entry
Database: EMDB / ID: EMD-19904
TitleC20 Vipp1 dL10Ala ring
Map data
Sample
  • Complex: Vipp1 dL10Ala
    • Protein or peptide: Vipp1 dL10Ala
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.0 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 20, 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_19904.png

Downloads & links

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Map

FileDownload / File: emd_19904.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.81 Å/pix.
x 450 pix.
= 814.5 Å		1.81 Å/pix.
x 450 pix.
= 814.5 Å		1.81 Å/pix.
x 450 pix.
= 814.5 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.1
Minimum - Maximum-0.52737707 - 2.3378572
Average (Standard dev.)0.022956539 (±0.15272157)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 814.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_19904_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_19904_half_map_2.map
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Sample components

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Entire : Vipp1 dL10Ala

EntireName: Vipp1 dL10Ala
Components
  • Complex: Vipp1 dL10Ala
    • Protein or peptide: Vipp1 dL10Ala

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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: Vipp1 dL10Ala

MacromoleculeName: Vipp1 dL10Ala / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
SequenceString: MGLFDRLGRV VRANLNDLVS KAEDPEKVLE QAVIDMQEDL VQLRQAVART IAEEKRTEQR LNQDTQEAKK WEDRAKLALT N GEENLARE ALARKKSLTD TAAAYQTQLA QQRTMSENLR RNLAALEAKI SEAKTKKNML QARAKAAKAN AELQQTLAAA AA AAAAAAF ...String:
MGLFDRLGRV VRANLNDLVS KAEDPEKVLE QAVIDMQEDL VQLRQAVART IAEEKRTEQR LNQDTQEAKK WEDRAKLALT N GEENLARE ALARKKSLTD TAAAYQTQLA QQRTMSENLR RNLAALEAKI SEAKTKKNML QARAKAAKAN AELQQTLAAA AA AAAAAAF ERMENKVLDM EATSQAAGEL AGFGIENQFA QLEASSGVED ELAALKASMA GGALPGTSAA TPQLEAAPVD SSVPANNASQ DDAVIDQELD DLRRRLNNLA ALEVLFQGP

UniProtKB: Membrane-associated protein Vipp1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle 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

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C20 (20 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 19580
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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