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- PDB-9gmb: MukEF in complex with the phage protein gp5.9 -

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Basic information

Entry
Database: PDB / ID: 9gmb
TitleMukEF in complex with the phage protein gp5.9
Components
  • Chromosome partition protein MukE
  • Chromosome partition protein MukF
  • Probable RecBCD inhibitor gp5.9
KeywordsDNA BINDING PROTEIN / SMC complex / Chromosome segregation / DNA mimic
Function / homology
Function and homology information


condensin complex / nucleoid / chromosome condensation / chromosome segregation / DNA replication / symbiont-mediated suppression of host innate immune response / cell division / calcium ion binding / cytoplasm
Similarity search - Function
Prokaryotic chromosome segregation/condensation protein MukE / MukE, C-terminal domain / MukE, N-terminal domain / MukE-like family / Chromosome partition protein MukF / Chromosome partition protein MukF, winged-helix domain / Chromosome partition protein MukF, middle domain / Chromosome partition protein MukF, C-terminal domain / MukF, middle domain superfamily / MukF, C-terminal domain superfamily ...Prokaryotic chromosome segregation/condensation protein MukE / MukE, C-terminal domain / MukE, N-terminal domain / MukE-like family / Chromosome partition protein MukF / Chromosome partition protein MukF, winged-helix domain / Chromosome partition protein MukF, middle domain / Chromosome partition protein MukF, C-terminal domain / MukF, middle domain superfamily / MukF, C-terminal domain superfamily / MukF winged-helix domain / MukF middle domain / MukF C-terminal domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Probable RecBCD inhibitor gp5.9 / Chromosome partition protein MukE / Chromosome partition protein MukF
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia phage T7 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsBurmann, F. / Wilkinson, O. / Kimanius, D. / Dillingham, M. / Lowe, J.
Funding supportEuropean Union, United Kingdom, 2items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)605-2019European Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/Y004426/1 United Kingdom
CitationJournal: Cell / Year: 2025
Title: Mechanism of DNA capture by the MukBEF SMC complex and its inhibition by a viral DNA mimic.
Authors: Frank Bürmann / Bryony Clifton / Sophie Koekemoer / Oliver J Wilkinson / Dari Kimanius / Mark S Dillingham / Jan Löwe /
Abstract: Ring-like structural maintenance of chromosome (SMC) complexes are crucial for genome organization and operate through mechanisms of DNA entrapment and loop extrusion. Here, we explore the DNA ...Ring-like structural maintenance of chromosome (SMC) complexes are crucial for genome organization and operate through mechanisms of DNA entrapment and loop extrusion. Here, we explore the DNA loading process of the bacterial SMC complex MukBEF. Using cryoelectron microscopy (cryo-EM), we demonstrate that ATP binding opens one of MukBEF's three potential DNA entry gates, exposing a DNA capture site that positions DNA at the open neck gate. We discover that the gp5.9 protein of bacteriophage T7 blocks this capture site by DNA mimicry, thereby preventing DNA loading and inactivating MukBEF. We propose a comprehensive and unidirectional loading mechanism in which DNA is first captured at the complex's periphery and then ingested through the DNA entry gate, powered by a single cycle of ATP hydrolysis. These findings illuminate a fundamental aspect of how ubiquitous DNA organizers are primed for genome maintenance and demonstrate how this process can be disrupted by viruses.
History
DepositionAug 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.2May 14, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Chromosome partition protein MukF
E: Chromosome partition protein MukE
F: Chromosome partition protein MukE
I: Probable RecBCD inhibitor gp5.9
J: Probable RecBCD inhibitor gp5.9
D: Chromosome partition protein MukF


Theoretical massNumber of molelcules
Total (without water)167,8066
Polymers167,8066
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 Chromosome partition protein MukF / Protein KicB


Mass: 50635.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mukF, kicB, b0922, JW0905 / Production host: Escherichia coli (E. coli) / References: UniProt: P60293
#2: Protein Chromosome partition protein MukE / Protein KicA


Mass: 27006.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mukE, kicA, ycbA, b0923, JW0906 / Production host: Escherichia coli (E. coli) / References: UniProt: P22524
#3: Protein Probable RecBCD inhibitor gp5.9 / Gene product 5.9 / Gp5.9


Mass: 6260.819 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage T7 (virus) / Gene: 5.9 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P20406
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: Reconstituted complex of gp5.9/MukEF / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.233 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/RHODIUM / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: NITROGEN

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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: 1000 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57528 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL

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