[English] 日本語
Yorodumi
- PDB-9qxr: E. coli JetABC monomer in a DNA boarding conformation -

+
Open data


ID or keywords:

Loading...

-
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: Mol Cell / Year: 2025
Title: Mechanism of DNA entrapment by a loop-extruding Wadjet SMC motor.
Authors: Florian Roisné-Hamelin / Hon Wing Liu / Nils Maréchal / Emiko Uchikawa / Alexandre Durand / Stephan Gruber /
Abstract: Structural maintenance of chromosome (SMC) complexes perform critical functions by folding DNA through loop extrusion. The choreography and outcome of SMC DNA loading prior to loop extrusion, ...Structural maintenance of chromosome (SMC) complexes perform critical functions by folding DNA through loop extrusion. The choreography and outcome of SMC DNA loading prior to loop extrusion, however, remain elusive. Here, we use cryo-electron microscopy to determine structures of the prokaryotic SMC Wadjet undergoing DNA loading. We show that an initial ATP-triggered relocation of both SMC dimers exposes a DNA-binding pocket and aligns two opened motor units on a DNA double helix. Subsequent ATP hydrolysis drives a nearly 360° rotation of each SMC dimer, closing the motor units around DNA in a sequential manner. This process leads to a DNA-holding conformation-an anticipated key intermediate in loop extrusion-with the DNA held within the kleisin/KITE sub-compartment. Our findings elucidate the mechanism of topological DNA loading by an SMC motor, revealing a straight DNA double helix with motor units oriented tail-to-tail in DNA-holding conformations as the likely starting point of DNA loop extrusion.
History
DepositionApr 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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)

-
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

-
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

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more