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- PDB-8qbr: Cryo-EM structure of Vipp1 helical filament with lattice 1 (Vipp1_L1) -

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Basic information

Entry
Database: PDB / ID: 8qbr
TitleCryo-EM structure of Vipp1 helical filament with lattice 1 (Vipp1_L1)
ComponentsMembrane-associated protein Vipp1
KeywordsLIPID BINDING PROTEIN / Vipp1/IM30/ESCRT-III / Membrane remodeling / Cryoelectron microscopy / Helical filament structure
Function / homologyPspA/IM30 / PspA/IM30 family / lipid binding / plasma membrane / Membrane-associated protein Vipp1
Function and homology information
Biological speciesNostoc punctiforme (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.74 Å
AuthorsNaskar, S. / Low, H.H.
Funding support United Kingdom, 1items
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, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 1.2Mar 26, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Membrane-associated protein Vipp1


Theoretical massNumber of molelcules
Total (without water)23,9621
Polymers23,9621
Non-polymers00
Water00
1
A: Membrane-associated protein Vipp1
x 95


Theoretical massNumber of molelcules
Total (without water)2,276,40095
Polymers2,276,40095
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation94
MethodUCSF CHIMERA

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Components

#1: Protein Membrane-associated protein Vipp1 / Vesicle-inducing protein in plastids 1 / Vipp1


Mass: 23962.100 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc punctiforme (bacteria) / Gene: vipp1, Npun_R3963 / Production host: Escherichia coli (E. coli) / References: UniProt: B2J6D9
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Vipp1_L1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Nostoc punctiforme (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8.4
SpecimenConc.: 1.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 750 nm
Image recordingElectron dose: 1.02 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
4RELION4CTF correctionCTFFIND4.1
7UCSF ChimeraX1.5model fitting
12RELION43D reconstruction
19Cootmodel refinement
20ISOLDEmodel refinement
21PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -75.860068 ° / Axial rise/subunit: 2.372081 Å / Axial symmetry: C1
3D reconstructionResolution: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43480 / Symmetry type: HELICAL
Atomic model buildingB value: 91.05 / Space: REAL

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