8QBV | pdb_00008qbv

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.78 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Mechanism for Vipp1 spiral formation, ring biogenesis, and membrane repair.

Naskar, S.Merino, A.Espadas, J.Singh, J.Roux, A.Colom, A.Low, H.H.

(2025) Nat Struct Mol Biol 32: 571-584

  • DOI: https://doi.org/10.1038/s41594-024-01401-8
  • Primary Citation of Related Structures:  
    8QBR, 8QBS, 8QBV, 8QBW

  • PubMed 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-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.


  • Organizational Affiliation
    • Department of Infectious Disease, Imperial College, London, UK.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Membrane-associated protein Vipp1217Nostoc punctiformeMutation(s): 0 
Gene Names: vipp1Npun_R3963
UniProt
Find proteins for B2J6D9 (Nostoc punctiforme (strain ATCC 29133 / PCC 73102))
Explore B2J6D9 
Go to UniProtKB:  B2J6D9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2J6D9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.78 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION4
MODEL REFINEMENTCoot
MODEL REFINEMENTISOLDE
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom215553/Z/19/Z

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-18
    Type: Initial release
  • Version 1.1: 2024-11-27
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2025-03-26
    Changes: Data collection, Database references