9QE1 | pdb_00009qe1

Neobacillus vireti Wadjet-II JetABC monomer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structure of a type II SMC Wadjet complex from Neobacillus vireti.

Roisne-Hamelin, F.Liu, H.W.Gruber, S.

(2025) Structure 33: 1498

  • DOI: https://doi.org/10.1016/j.str.2025.06.004

  • PubMed 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 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.


  • Organizational Affiliation
    • Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), 1015 Lausanne, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 490.18 kDa 
  • Atom Count: 30,006 
  • Modeled Residue Count: 3,590 
  • Deposited Residue Count: 4,131 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
JetC
A, B
1,371Neobacillus vireti LMG 21834Mutation(s): 0 
Gene Names: JetC
UniProt
Find proteins for A0AB94IPK1 (Neobacillus vireti LMG 21834)
Explore A0AB94IPK1 
Go to UniProtKB:  A0AB94IPK1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AB94IPK1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
JetBC [auth D]389Neobacillus vireti LMG 21834Mutation(s): 0 
Gene Names: JetB
UniProt
Find proteins for A0AB94IPP4 (Neobacillus vireti LMG 21834)
Explore A0AB94IPP4 
Go to UniProtKB:  A0AB94IPP4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AB94IPP4
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
JetAD [auth E],
E [auth J]
500Neobacillus vireti LMG 21834Mutation(s): 0 
Gene Names: JetC
UniProt
Find proteins for A0AB94IPG3 (Neobacillus vireti LMG 21834)
Explore A0AB94IPG3 
Go to UniProtKB:  A0AB94IPG3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AB94IPG3
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union724482
Swiss National Science FoundationSwitzerland10001017

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-25
    Type: Initial release
  • Version 1.1: 2025-07-23
    Changes: Data collection, Database references
  • Version 1.2: 2025-09-17
    Changes: Data collection, Database references