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- PDB-9qe0: Neobacillus vireti Wadjet-II JetABC dimer -

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Basic information

Entry
Database: PDB / ID: 9qe0
TitleNeobacillus vireti Wadjet-II JetABC dimer
Components
  • JetA
  • JetB
  • JetC
KeywordsDNA BINDING PROTEIN / SMC complexes / Wadjet / JetABCD / DNA loop extrusion
Biological speciesNeobacillus vireti LMG 21834 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.71 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: To Be Published
Title: Structure of a type II SMC Wadjet complex from Neobacillus vireti
Authors: Roisne-Hamelin, F. / Liu, H.W. / Gruber, S.
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
Revision 1.0Jun 25, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: JetC
B: JetC
D: JetB
E: JetA
F: JetC
G: JetC
H: JetB
J: JetA


Theoretical massNumber of molelcules
Total (without water)859,2158
Polymers859,2158
Non-polymers00
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.: 4
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)
Production host: Escherichia coli BL21 (bacteria)
#2: Protein JetB


Mass: 46569.652 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)
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)
Production host: Escherichia coli BL21 (bacteria)
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: all / 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
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 softwareName: PHENIX / Version: 1.21.2_5419: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 6.71 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15908 / 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_d0.00561318
ELECTRON MICROSCOPYf_angle_d1.0582568
ELECTRON MICROSCOPYf_dihedral_angle_d5.277930
ELECTRON MICROSCOPYf_chiral_restr0.0558738
ELECTRON MICROSCOPYf_plane_restr0.00610804

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