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

Validation slider image for 9GMB

This is version 1.2 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 188: 2465

  • DOI: https://doi.org/10.1016/j.cell.2025.02.032
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 167.81 kDa 
  • Atom Count: 9,002 
  • Modeled Residue Count: 1,111 
  • Deposited Residue Count: 1,458 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
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
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Reference Sequence
Find similar proteins by:|  3D Structure
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
Entity Groups
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UniProt GroupP22524
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Reference Sequence
Find similar proteins by:|  3D Structure
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

View Full Validation Report



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
  • Version 1.2: 2025-05-14
    Changes: Data collection, Database references