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- EMDB-54678: S. islandicus CdvA filament (cryo-EM) -

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Basic information

Entry
Database: EMDB / ID: EMD-54678
TitleS. islandicus CdvA filament (cryo-EM)
Map datapost-processed map with imposed helical symmetry and corrected handedness
Sample
  • Complex: helical filament of CdvA
    • Protein or peptide: Cell division protein CdvA
Keywordscell division / archaea / CELL CYCLE
Function / homologyCdvA-like coiled-coil domain / : / CdvA-like coiled-coil domain / cell division / Cell division protein CdvA
Function and homology information
Biological speciesSaccharolobus islandicus (archaea)
Methodhelical reconstruction / cryo EM / Resolution: 4.07 Å
AuthorsSalzer R / Lowe J
Funding support United Kingdom, Germany, 6 items
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
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, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54678.png

Downloads & links

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Map

FileDownload / File: emd_54678.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpost-processed map with imposed helical symmetry and corrected handedness
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 320 pix.
= 341.76 Å		1.07 Å/pix.
x 320 pix.
= 341.76 Å		1.07 Å/pix.
x 320 pix.
= 341.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.022
Minimum - Maximum-0.027393114 - 0.08430493
Average (Standard dev.)-0.000019953106 (±0.0024785704)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 341.75998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Raw Refine3D map

Fileemd_54678_additional_1.map
AnnotationRaw Refine3D map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_54678_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_54678_half_map_2.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : helical filament of CdvA

EntireName: helical filament of CdvA
Components
  • Complex: helical filament of CdvA
    • Protein or peptide: Cell division protein CdvA

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Supramolecule #1: helical filament of CdvA

SupramoleculeName: helical filament of CdvA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharolobus islandicus (archaea)

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Macromolecule #1: Cell division protein CdvA

MacromoleculeName: Cell division protein CdvA / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus islandicus (archaea)
Molecular weightTheoretical: 27.175277 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MPVSYEVLTK FIGQKVKDIY GREFGYLIHV YSEIDGSITG IEVAQGSSIL TMGPERIKLD GDSILILPDW KAEAIRILSL MEKIRKRQR ALEELYNKQE IPKSDYDDMK RKLDTEMLKV KDDQNKLKGK LKSRLNDIED QLAHIDKAVI SLKMSYISSE I PENAYKGS ...String:
MPVSYEVLTK FIGQKVKDIY GREFGYLIHV YSEIDGSITG IEVAQGSSIL TMGPERIKLD GDSILILPDW KAEAIRILSL MEKIRKRQR ALEELYNKQE IPKSDYDDMK RKLDTEMLKV KDDQNKLKGK LKSRLNDIED QLAHIDKAVI SLKMSYISSE I PENAYKGS MEVLRQSKDS YTLERDDIRK TLDRLDSLDK ESIELKPLGS LSTSQQGEAK SDQSKSEIPL PIPVKVINTL

UniProtKB: Cell division protein CdvA

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8 / Details: 30 mM Tris/HCl, 150 mM NaCl, 4 mM TCEP
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 63.702 Å
Applied symmetry - Helical parameters - Δ&Phi: 48.9227 °
Applied symmetry - Helical parameters - Axial symmetry: D1 (2x1 fold dihedral)
Resolution.type: BY AUTHOR / Resolution: 4.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 253803
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9s9g

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

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Atomic model buiding 1

Initial modelPDB ID:

9s9g


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-9s9h:
S. islandicus CdvA filament (cryo-EM)

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