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- PDB-9s9j: S. islandicus CdvB (closed) -

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Basic information

Entry
Database: PDB / ID: 9s9j
TitleS. islandicus CdvB (closed)
ComponentsCell division protein CdvB, Vps2 like protein
KeywordsCELL CYCLE / cell division / archaea
Function / homology: / Winged helix-like DNA-binding domain superfamily / cell division / Cell division protein CdvB, Vps2 like protein
Function and homology information
Biological speciesSaccharolobus islandicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsSalzer, R. / Lowe, J.
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 CdvB, Vps2 like protein


Theoretical massNumber of molelcules
Total (without water)21,9721
Polymers21,9721
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10580 Å2
Unit cell
Length a, b, c (Å)59.354, 59.354, 124.368
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Cell division protein CdvB, Vps2 like protein


Mass: 21972.072 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminal truncation (deleted residues 206-259). Mutations: I69M, I125M
Source: (gene. exp.) Saccharolobus islandicus (archaea) / Gene: SiRe_1174 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: F0NEW1
Has protein modificationY

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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: 2.49 Å3/Da / Density % sol: 50.65 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 5% (v/v) 2-propanol, 1M ammonium sulphate or 0.2 M ammonium sulphate, 15% (w/v) PEG 4000, pH 3.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97942 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.6→42.94 Å / Num. obs: 34815 / % possible obs: 100 % / Redundancy: 12.4 % / CC1/2: 1 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.019 / Rrim(I) all: 0.065 / Net I/σ(I): 23.8
Reflection shellResolution: 2.6→2.74 Å / % possible obs: 100 % / Redundancy: 13.2 % / Rmerge(I) obs: 2.074 / Num. measured all: 13574 / Num. unique obs: 1026 / CC1/2: 0.461 / Rpim(I) all: 0.61 / Rrim(I) all: 2.233 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
PHENIX(dev_2919)refinement
SCALAdata scaling
PDB_EXTRACTdata extraction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→42.935 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 0.34 / Phase error: 33.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2656 587 5.04 %
Rwork0.2434 --
obs0.2445 11653 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→42.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1352 0 0 0 1352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071360
X-RAY DIFFRACTIONf_angle_d0.951826
X-RAY DIFFRACTIONf_dihedral_angle_d11.225876
X-RAY DIFFRACTIONf_chiral_restr0.049223
X-RAY DIFFRACTIONf_plane_restr0.004232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.97170.381590.32252759X-RAY DIFFRACTION100
2.9717-3.40160.35961740.28872725X-RAY DIFFRACTION100
3.4016-4.2850.26591210.25722800X-RAY DIFFRACTION100
4.285-42.9350.2281330.21942782X-RAY DIFFRACTION100

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