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- PDB-9s9i: S. islandicus CdvA (non-polymerising mutant) -

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Basic information

Entry
Database: PDB / ID: 9s9i
TitleS. islandicus CdvA (non-polymerising mutant)
ComponentsCell division protein CdvA
KeywordsCELL CYCLE / cell division / archaea
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)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSalzer, R. / Lowe, J. / Bellini, D.
Funding support United Kingdom, Germany, 6items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2026Provider: 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 CdvA
B: Cell division protein CdvA


Theoretical massNumber of molelcules
Total (without water)54,4222
Polymers54,4222
Non-polymers00
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-1 kcal/mol
Surface area23430 Å2
Unit cell
Length a, b, c (Å)66.330, 78.680, 93.280
Angle α, β, γ (deg.)90.00, 104.63, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-312-

HOH

21B-301-

HOH

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Components

#1: Protein Cell division protein CdvA


Mass: 27210.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: mutations: A90D, L94D, I100D, I149D, M153D, I156D / Source: (gene. exp.) Saccharolobus islandicus (archaea) / Gene: SiL_1169 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: M9U931
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 18 % (w/v) PEG 4000, 0.3 M sodium acetate, 0.1 M Tris pH 9.0.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.2→22.85 Å / Num. obs: 22835 / % possible obs: 96.5 % / Redundancy: 3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.043 / Rrim(I) all: 0.077 / Χ2: 1 / Net I/σ(I): 9.7 / Num. measured all: 69155
Reflection shellResolution: 2.2→2.26 Å / % possible obs: 91.5 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.71 / Num. measured all: 4401 / Num. unique obs: 1601 / CC1/2: 0.727 / Rpim(I) all: 0.486 / Rrim(I) all: 0.864 / Χ2: 0.79 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→22.85 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.259 1179 5.16 %
Rwork0.2279 --
obs0.2294 22832 96.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→22.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3110 0 0 78 3188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013145
X-RAY DIFFRACTIONf_angle_d1.3534209
X-RAY DIFFRACTIONf_dihedral_angle_d22.012422
X-RAY DIFFRACTIONf_chiral_restr0.072468
X-RAY DIFFRACTIONf_plane_restr0.008540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.30.37521610.33762615X-RAY DIFFRACTION95
2.3-2.420.35341380.30692783X-RAY DIFFRACTION99
2.42-2.570.31871770.30122748X-RAY DIFFRACTION99
2.57-2.770.351490.30032739X-RAY DIFFRACTION99
2.77-3.050.31941450.26942740X-RAY DIFFRACTION97
3.05-3.490.27131340.23482705X-RAY DIFFRACTION97
3.49-4.390.24021330.19732636X-RAY DIFFRACTION93
4.39-22.850.18961420.18282687X-RAY DIFFRACTION94

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