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- PDB-9gm7: MukBEF in a nucleotide-bound state with open neck gate (monomer) -

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Basic information

Entry
Database: PDB / ID: 9gm7
TitleMukBEF in a nucleotide-bound state with open neck gate (monomer)
Components
  • (Chromosome partition protein ...) x 3
  • Acyl carrier protein
KeywordsDNA BINDING PROTEIN / SMC complex / Chromosome segregation / ABC-type ATPase
Function / homology
Function and homology information


nucleoid / chromosome condensation / lipid biosynthetic process / lipid A biosynthetic process / acyl binding / acyl carrier activity / phosphopantetheine binding / chromosome segregation / fatty acid biosynthetic process / DNA replication ...nucleoid / chromosome condensation / lipid biosynthetic process / lipid A biosynthetic process / acyl binding / acyl carrier activity / phosphopantetheine binding / chromosome segregation / fatty acid biosynthetic process / DNA replication / response to xenobiotic stimulus / cell division / lipid binding / calcium ion binding / DNA binding / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
Prokaryotic chromosome segregation/condensation protein MukE / MukB, N-terminal domain / Chromosome partition protein MukB / MukB, hinge domain / MukE, C-terminal domain / MukE, N-terminal domain / MukB, hinge domain superfamily / : / MukE-like family / MukB N-terminal ...Prokaryotic chromosome segregation/condensation protein MukE / MukB, N-terminal domain / Chromosome partition protein MukB / MukB, hinge domain / MukE, C-terminal domain / MukE, N-terminal domain / MukB, hinge domain superfamily / : / MukE-like family / MukB N-terminal / MukB hinge domain / 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 / SbcC/RAD50-like, Walker B motif / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Chromosome partition protein MukF / Chromosome partition protein MukE / Chromosome partition protein MukB / Acyl carrier protein
Similarity search - Component
Biological speciesPhotorhabdus thracensis (bacteria)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsBurmann, F. / Lowe, J.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)ALTF 605-2019European Union
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: 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
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Revision 1.2May 14, 2025Group: Data collection / Database references / Category: citation / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Chromosome partition protein MukF
D: Chromosome partition protein MukF
E: Chromosome partition protein MukE
F: Chromosome partition protein MukE
G: Acyl carrier protein
I: Acyl carrier protein
A: Chromosome partition protein MukB
B: Chromosome partition protein MukB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)514,75112
Polymers513,6888
Non-polymers1,0634
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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Chromosome partition protein ... , 3 types, 6 molecules CDEFAB

#1: Protein Chromosome partition protein MukF


Mass: 50193.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus thracensis (bacteria) / Gene: mukF, VY86_15860 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F7LMQ4
#2: Protein Chromosome partition protein MukE


Mass: 27423.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus thracensis (bacteria) / Gene: mukE, VY86_15865 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F7LPV6
#4: Protein Chromosome partition protein MukB / Structural maintenance of chromosome-related protein


Mass: 170241.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus thracensis (bacteria) / Gene: mukB, VY86_15870 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F7LRY2

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Protein , 1 types, 2 molecules GI

#3: Protein Acyl carrier protein / ACP / Cytosolic-activating factor / CAF / Fatty acid synthase acyl carrier protein


Mass: 8985.794 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: acpP, b1094, JW1080 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6A8

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Non-polymers , 2 types, 4 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM

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Details

Has ligand of interestY
Has protein modificationY

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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: MukBEF DNA loading reaction / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 0.924253 MDa / Experimental value: NO
Source (natural)Organism: Photorhabdus thracensis (bacteria)
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: GOLD / Grid mesh size: 200 divisions/in. / Grid type: UltrAuFoil 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

EM softwareName: cryoSPARC / Category: 3D reconstruction / Details: 3DFlex
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34436 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL

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