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- PDB-9qe1: Neobacillus vireti Wadjet-II JetABC monomer -

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Basic information

Entry
Database: PDB / ID: 9qe1
TitleNeobacillus vireti Wadjet-II JetABC monomer
Components
  • JetA
  • JetB
  • JetC
KeywordsDNA BINDING PROTEIN / SMC complexes / Wadjet / JetABCD / DNA loop extrusion
Function / homologyADENOSINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesNeobacillus vireti LMG 21834 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsRoisne-Hamelin, F. / Gruber, S.
Funding supportEuropean Union, Switzerland, 2items
OrganizationGrant numberCountry
European Research Council (ERC)724482European Union
Swiss National Science Foundation10001017 Switzerland
CitationJournal: Structure / Year: 2025
Title: Structure of a type II SMC Wadjet complex from Neobacillus vireti.
Authors: Florian Roisné-Hamelin / Hon Wing Liu / Stephan Gruber /
Abstract: Structural maintenance of chromosome complexes are essential DNA-folding motors that facilitate critical cellular functions, including chromosome segregation and DNA repair. Wadjet systems are ...Structural maintenance of chromosome complexes are essential DNA-folding motors that facilitate critical cellular functions, including chromosome segregation and DNA repair. Wadjet systems are prokaryotic SMC complexes specialized in cellular immunity against plasmids. Type I Wadjet systems restrict plasmids via a DNA extrusion-cleavage reaction. Two other Wadjet types (II and III) have also been identified, however, their molecular characteristics are unclear. Here, we reconstituted a representative type II Wadjet system from Neobacillus vireti. We show that this system shares substrate selection and cleavage properties with type I but exhibits distinctive structural features, including a long elbow-distal coiled coil, a channel-less hinge, and a tandem KITE subunit. These features help identify the common and distinguishing architectural elements in the family of Wadjet systems and raise intriguing questions about the evolution of prokaryotic SMC complexes.
History
DepositionMar 7, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.2Sep 17, 2025Group: Data collection / Database references / Category: citation / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: JetC
B: JetC
D: JetB
E: JetA
J: JetA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)490,1817
Polymers489,3275
Non-polymers8542
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein JetC


Mass: 161659.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The last "G" in the theorical sequence is the result of a DNA cloning scar.
Source: (gene. exp.) Neobacillus vireti LMG 21834 (bacteria)
Gene: JetC / Production host: Escherichia coli BL21 (bacteria)
#2: Protein JetB


Mass: 46569.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The last "G" in the theorical sequence is the result of a DNA cloning scar.
Source: (gene. exp.) Neobacillus vireti LMG 21834 (bacteria)
Gene: JetB / Production host: Escherichia coli BL21 (bacteria)
#3: Protein JetA


Mass: 59719.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: "GPAA" at the begining of the theorical sequence is the remaining of the purification tag after tag cleavage. The last "G" in the theorical sequence is the result of a DNA cloning scar.
Source: (gene. exp.) Neobacillus vireti LMG 21834 (bacteria)
Gene: JetC / Production host: Escherichia coli BL21 (bacteria)
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: N. vireti JetABC dimer-of-tetramers / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Neobacillus vireti LMG 21834 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21 (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: Au-flat 1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K

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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: 800 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 22188

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7ISOLDEmodel fitting
8Cootmodel fitting
13cryoSPARC3D reconstruction
14PHENIX1.20.1_4487:model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47279 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00430601
ELECTRON MICROSCOPYf_angle_d0.53241219
ELECTRON MICROSCOPYf_dihedral_angle_d4.8913953
ELECTRON MICROSCOPYf_chiral_restr0.0344360
ELECTRON MICROSCOPYf_plane_restr0.0035384

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