9GMB | pdb_00009gmb

MukEF in complex with the phage protein gp5.9


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Mechanism of DNA capture by the MukBEF SMC complex and its inhibition by a viral DNA mimic.

Burmann, F.Clifton, B.Koekemoer, S.Wilkinson, O.J.Kimanius, D.Dillingham, M.S.Lowe, J.

(2025) Cell 

  • DOI: https://doi.org/10.1016/j.cell.2025.02.032
  • Primary Citation of Related Structures:  
    9GM6, 9GM7, 9GM8, 9GM9, 9GMA, 9GMB, 9GMD

  • PubMed 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 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.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Structural Studies, Francis Crick Avenue, Cambridge CB2 0QH, UK; University of Oxford, Department of Biochemistry, South Parks Road, Oxford OX1 3QU, UK. Electronic address: frank.burmann@bioch.ox.ac.uk.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chromosome partition protein MukFA [auth C],
F [auth D]
440Escherichia coliMutation(s): 0 
Gene Names: mukFkicBb0922JW0905
UniProt
Find proteins for P60293 (Escherichia coli (strain K12))
Explore P60293 
Go to UniProtKB:  P60293
Entity Groups  
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UniProt GroupP60293
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Chromosome partition protein MukEB [auth E],
C [auth F]
234Escherichia coliMutation(s): 0 
Gene Names: mukEkicAycbAb0923JW0906
UniProt
Find proteins for P22524 (Escherichia coli (strain K12))
Explore P22524 
Go to UniProtKB:  P22524
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UniProt GroupP22524
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Probable RecBCD inhibitor gp5.9D [auth I],
E [auth J]
55Escherichia phage T7Mutation(s): 0 
Gene Names: 5.9
UniProt
Find proteins for P20406 (Escherichia phage T7)
Explore P20406 
Go to UniProtKB:  P20406
Entity Groups  
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UniProt GroupP20406
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Molecular Biology Organization (EMBO)European Union605-2019
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/Y004426/1

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-26
    Type: Initial release
  • Version 1.1: 2025-04-16
    Changes: Data collection, Database references