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- PDB-9s98: CdvB2 filament - high twist, class A -

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Basic information

Entry
Database: PDB / ID: 9s98
TitleCdvB2 filament - high twist, class A
ComponentsCell division protein B2
KeywordsCELL CYCLE / cell division / ESCRT-III / membrane remodelling / archaea
Function / homology: / cell division / Cell division protein B2
Function and homology information
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.86 Å
AuthorsDrobnic, T. / Lowe, J.
Funding support United Kingdom, Germany, 7items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)U105184326 United Kingdom
Wellcome Trust227876/Z/23/Z United Kingdom
Wellcome Trust203276/Z/16/Z United Kingdom
Volkswagen Foundation94933 Germany
Wellcome Trust222460/Z/21/Z United Kingdom
UK Research and Innovation (UKRI)MC_UP_1201/27 United Kingdom
German Research Foundation (DFG)CIBSS - EXC-2189 - Project ID 390939984 Germany
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Molecular structure of the ESCRT-III-based archaeal CdvAB cell division machinery.
Authors: Tina Drobnič / Ralf Salzer / Tim Nierhaus / Margaret Ke Xin Jiang / Dom Bellini / Astrid Steindorf / Sonja-Verena Albers / Buzz Baum / Jan Löwe /
Abstract: Most prokaryotes divide using filaments of the tubulin-like FtsZ protein, while some archaea employ instead ESCRT-III-like proteins and their filaments for cell division and cytokinesis. The ...Most prokaryotes divide using filaments of the tubulin-like FtsZ protein, while some archaea employ instead ESCRT-III-like proteins and their filaments for cell division and cytokinesis. The alternative archaeal system comprises Cdv proteins and is thought to bear some resemblance to ESCRT-III-based membrane remodeling in other domains of life, including eukaryotes, especially during abscission. Here, we present biochemical, crystallographic, and cryo-EM studies of the Cdv machinery. CdvA, an early non-ESCRT component, adopts a PRC-domain/coiled-coil fold and polymerizes into long double-stranded helical filaments, mainly via hydrophobic interfaces. Monomeric CdvB adopts the canonical ESCRT-III fold in both a closed and a distinct "semiopen" conformation. Soluble CdvB2 filaments are composed of subunits in the closed state, appearing to transition to the open, active state only when polymerized on membranes. Short N-terminal amphipathic helices in all CdvB paralogues, B, B1, and B2, mediate membrane binding and are required for liposome recruitment in vitro. We provide a molecular overview of archaeal ESCRT-III-based cytokinesis machinery, the definitive demonstration that CdvB proteins are bona fide ESCRT-III homologues, and reveal the molecular basis for membrane engagement. Thus, we illuminate conserved principles of ESCRT-mediated membrane remodeling and extend them to an anciently diverged archaeal lineage.
History
DepositionAug 6, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell division protein B2
B: Cell division protein B2
C: Cell division protein B2


Theoretical massNumber of molelcules
Total (without water)74,6473
Polymers74,6473
Non-polymers00
Water00
1
A: Cell division protein B2
B: Cell division protein B2
C: Cell division protein B2
x 6


Theoretical massNumber of molelcules
Total (without water)447,88518
Polymers447,88518
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5

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Components

#1: Protein Cell division protein B2 / ESCRT-III homolog


Mass: 24882.492 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Strain: MW001 / Gene: cdvB2, Saci_1416 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE2) / References: UniProt: Q4J8Y4
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: Filament of purified CdvB2 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Sulfolobus acidocaldarius (acidophilic) / Strain: MW001
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: C43(DE3)
Buffer solutionpH: 6 / Details: 50 mM MES, 50 mM NaCl
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 35.86 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1crYOLO1.9.6particle selection
2EPUimage acquisition
4CTFFIND4.1CTF correction
7UCSF ChimeraX1.6.1model fitting
12RELION43D reconstruction
13PHENIX1.21.2_5419:model refinement
14Coot0.9.8.2model refinement
15ISOLDE1.6model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 176.242 ° / Axial rise/subunit: 18.8232 Å / Axial symmetry: C1
3D reconstructionResolution: 3.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 139884 / Symmetry type: HELICAL
Atomic model buildingProtocol: AB INITIO MODEL
Atomic model buildingDetails: ModelAngelo / Source name: Other / Type: other

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