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- PDB-9s9g: S. islandicus CdvA filament (X-ray) -

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Basic information

Entry
Database: PDB / ID: 9s9g
TitleS. islandicus CdvA filament (X-ray)
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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
C: Cell division protein CdvA
D: Cell division protein CdvA
E: Cell division protein CdvA
F: Cell division protein CdvA
G: Cell division protein CdvA
H: Cell division protein CdvA
I: Cell division protein CdvA
J: Cell division protein CdvA
K: Cell division protein CdvA
L: Cell division protein CdvA
M: Cell division protein CdvA
N: Cell division protein CdvA


Theoretical massNumber of molelcules
Total (without water)380,45414
Polymers380,45414
Non-polymers00
Water00
1
A: Cell division protein CdvA
B: Cell division protein CdvA


Theoretical massNumber of molelcules
Total (without water)54,3512
Polymers54,3512
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-16 kcal/mol
Surface area22900 Å2
2
C: Cell division protein CdvA
G: Cell division protein CdvA


Theoretical massNumber of molelcules
Total (without water)54,3512
Polymers54,3512
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-18 kcal/mol
Surface area22520 Å2
3
D: Cell division protein CdvA
F: Cell division protein CdvA


Theoretical massNumber of molelcules
Total (without water)54,3512
Polymers54,3512
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-16 kcal/mol
Surface area22910 Å2
4
E: Cell division protein CdvA

H: Cell division protein CdvA


Theoretical massNumber of molelcules
Total (without water)54,3512
Polymers54,3512
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area2690 Å2
ΔGint-16 kcal/mol
Surface area23110 Å2
5
I: Cell division protein CdvA

K: Cell division protein CdvA


Theoretical massNumber of molelcules
Total (without water)54,3512
Polymers54,3512
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area2580 Å2
ΔGint-16 kcal/mol
Surface area22520 Å2
6
J: Cell division protein CdvA

L: Cell division protein CdvA


Theoretical massNumber of molelcules
Total (without water)54,3512
Polymers54,3512
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area2720 Å2
ΔGint-14 kcal/mol
Surface area22740 Å2
7
M: Cell division protein CdvA
N: Cell division protein CdvA


Theoretical massNumber of molelcules
Total (without water)54,3512
Polymers54,3512
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-17 kcal/mol
Surface area22650 Å2
Unit cell
Length a, b, c (Å)71.032, 102.716, 328.554
Angle α, β, γ (deg.)90.00, 92.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cell division protein CdvA


Mass: 27175.277 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharolobus islandicus (archaea) / Gene: SiL_1169 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: M9U931
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: 3.15 Å3/Da / Density % sol: 60.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.282 M KH2PO4, 0.094 M Tris/acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97953 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97953 Å / Relative weight: 1
ReflectionResolution: 2.38→325.96 Å / Num. obs: 183198 / % possible obs: 98.5 % / Redundancy: 26.2 % / CC1/2: 0.672 / Rmerge(I) obs: 1.666 / Rpim(I) all: 0.358 / Rrim(I) all: 1.711 / Χ2: 0.95 / Net I/σ(I): 1.5 / Num. measured all: 4796820
Reflection shellResolution: 2.38→2.51 Å / Redundancy: 19.1 % / Num. unique obs: 25112 / CC1/2: 0.137 / Rpim(I) all: 3.78 / Rrim(I) all: 16.086 / Χ2: 0.87

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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: 2.85→52.62 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 43.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.298 1870 5.1 %
Rwork0.2261 --
obs0.2299 36663 33.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→52.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21978 0 0 0 21978
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01122231
X-RAY DIFFRACTIONf_angle_d1.43229750
X-RAY DIFFRACTIONf_dihedral_angle_d21.7758927
X-RAY DIFFRACTIONf_chiral_restr0.073346
X-RAY DIFFRACTIONf_plane_restr0.0083766
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.930.011130.62744X-RAY DIFFRACTION1
2.93-3.010.852390.4794149X-RAY DIFFRACTION2
3.01-3.110.7075140.4708309X-RAY DIFFRACTION4
3.11-3.220.4291310.4414600X-RAY DIFFRACTION7
3.22-3.350.4522420.3867870X-RAY DIFFRACTION11
3.35-3.50.3442440.38131143X-RAY DIFFRACTION14
3.5-3.690.4208800.30361530X-RAY DIFFRACTION19
3.69-3.920.34971150.2842011X-RAY DIFFRACTION25
3.92-4.220.3251590.22952861X-RAY DIFFRACTION36
4.22-4.650.27982280.19134000X-RAY DIFFRACTION50
4.65-5.320.28692610.20675437X-RAY DIFFRACTION67
5.32-6.70.34114270.2767843X-RAY DIFFRACTION97
6.7-52.620.25834570.19567996X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -5.7857 Å / Origin y: -5.0924 Å / Origin z: 84.4224 Å
111213212223313233
T0.3152 Å2-0.0251 Å20.026 Å2-0.2213 Å20.0248 Å2--0.3372 Å2
L0.3105 °20.0482 °20.0822 °2-0.1013 °20.0626 °2--0.1725 °2
S-0.018 Å °0.0611 Å °-0.0334 Å °-0.0469 Å °0.0245 Å °-0.0526 Å °0.0083 Å °0.0945 Å °-0.0015 Å °
Refinement TLS groupSelection details: all

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