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- PDB-9qxr: E. coli JetABC monomer in a DNA boarding conformation -

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Basic information

Entry
Database: PDB / ID: 9qxr
TitleE. coli JetABC monomer in a DNA boarding conformation
Components
  • Biotinylated circular plasmid DNA (1894-MER)
  • JetA
  • JetB
  • JetC
KeywordsDNA BINDING PROTEIN / SMC complexes / Wadjet / JetABCD / DNA loop extrusion
Function / homologyADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DNA / DNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.25 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: Molecular Cell / Year: 2025
Title: Mechanism of DNA Entrapment by a Loop-Extruding Wadjet SMC Motor
Authors: Roisne-Hamelin, F. / Liu, H.W. / Gruber, S.
History
DepositionApr 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: JetB
D: JetB
E: JetA
J: JetA
A: JetC
B: JetC
P: Biotinylated circular plasmid DNA (1894-MER)
Q: Biotinylated circular plasmid DNA (1894-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)458,79414
Polymers457,7598
Non-polymers1,0356
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

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Protein , 3 types, 6 molecules CDEJAB

#1: Protein JetB


Mass: 28020.416 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.) Escherichia coli (E. coli) / Strain: GF4-3 / Gene: ECIG_04711 / Production host: Escherichia coli BL21 (bacteria)
#2: Protein JetA / QJU27022.1


Mass: 57818.910 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. "GPAA" at the begining of the theorical sequence is the remaining of the purification tag after tag cleavage. The ...Details: The last "G" in the theorical sequence is the result of a DNA cloning scar. "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.) Escherichia coli (E. coli) / Strain: GF4-3 / Gene: GP975_00950 / Production host: Escherichia coli BL21 (bacteria)
#3: Protein JetC


Mass: 124562.938 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.) Escherichia coli (E. coli) / Strain: GF4-3 / Gene: GP975_00960 / Production host: Escherichia coli BL21 (bacteria)

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DNA chain , 1 types, 2 molecules PQ

#4: DNA chain Biotinylated circular plasmid DNA (1894-MER)


Mass: 18477.025 Da / Num. of mol.: 2 / Mutation: The DNA was modelled as polyAT track.
Source method: isolated from a genetically manipulated source
Details: Only a portion of the biotinylated plasmid (pSG7427, 1894bp) has been modelled as polyAT track, because the complex is expected to load at random positions and the local resolution of the ...Details: Only a portion of the biotinylated plasmid (pSG7427, 1894bp) has been modelled as polyAT track, because the complex is expected to load at random positions and the local resolution of the DNA does not allow any sequence assignment.
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / Strain (production host): pirHC

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Non-polymers , 3 types, 6 molecules

#5: 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
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3

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Details

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: JetABC DNA boarding state, a step of the loading reaction on DNA
Type: COMPLEX
Details: E. coli JetABC was incubated with biotinylated plasmid DNA in presence of ATP. The reaction was poisoned with beryllium fluoride prior grid freezing.
Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: GF4-3
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: Escherichia coli (BL21)
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: 279 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: 2400 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 39.48 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 31601

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Processing

EM software
IDNameVersionCategory
12cryoSPARC3D reconstruction
13PHENIX1.21.2_5419:model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 78524 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Atomic model building

3D fitting-ID: 1

IDPDB-IDAccession codeInitial refinement model-IDSource nameTypeDetails
18as8

8as8

8as81PDBexperimental model
28bfn

8bfn

8bfn2PDBexperimental model
38q72

8q72

8q72PDBexperimental model
4Otherin silico modelIdealized B-form DNA was flexibly fitted
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00324896
ELECTRON MICROSCOPYf_angle_d0.54834191
ELECTRON MICROSCOPYf_dihedral_angle_d17.6944456
ELECTRON MICROSCOPYf_chiral_restr0.0373839
ELECTRON MICROSCOPYf_plane_restr0.0034069

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