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- EMDB-51447: MukEF in complex with the phage protein gp5.9 -

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Basic information

Entry
Database: EMDB / ID: EMD-51447
TitleMukEF in complex with the phage protein gp5.9
Map dataPrimary map
Sample
  • Complex: Reconstituted complex of gp5.9/MukEF
    • Protein or peptide: Chromosome partition protein MukF
    • Protein or peptide: Chromosome partition protein MukE
    • Protein or peptide: Probable RecBCD inhibitor gp5.9
KeywordsSMC complex / Chromosome segregation / DNA mimic / DNA BINDING PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsBurmann F / Wilkinson O / Kimanius D / Dillingham M / Lowe J
Funding supportEuropean Union, United Kingdom, 2 items
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, 2024-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51447.png

Downloads & links

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Map

FileDownload / File: emd_51447.map.gz / Format: CCP4 / Size: 35.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.42 Å/pix.
x 210 pix.
= 298.815 Å		1.42 Å/pix.
x 210 pix.
= 298.815 Å		1.42 Å/pix.
x 210 pix.
= 298.815 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.42293 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.019885592 - 0.05103972
Average (Standard dev.)0.0000035603841 (±0.00131335)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions210210210
Spacing210210210
CellA=B=C: 298.8153 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51447_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map

Fileemd_51447_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1

Fileemd_51447_half_map_1.map
AnnotationHalf-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2

Fileemd_51447_half_map_2.map
AnnotationHalf-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Reconstituted complex of gp5.9/MukEF

EntireName: Reconstituted complex of gp5.9/MukEF
Components
  • Complex: Reconstituted complex of gp5.9/MukEF
    • Protein or peptide: Chromosome partition protein MukF
    • Protein or peptide: Chromosome partition protein MukE
    • Protein or peptide: Probable RecBCD inhibitor gp5.9

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Supramolecule #1: Reconstituted complex of gp5.9/MukEF

SupramoleculeName: Reconstituted complex of gp5.9/MukEF / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 233 KDa

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Macromolecule #1: Chromosome partition protein MukF

MacromoleculeName: Chromosome partition protein MukF / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 50.635727 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSEFSQTVPE LVAWARKNDF SISLPVDRLS FLLAVATLNG ERLDGEMSEG ELVDAFRHVS DAFEQTSETI GVRANNAIND MVRQRLLNR FTSEQAEGNA IYRLTPLGIG ITDYYIRQRE FSTLRLSMQL SIVAGELKRA ADAAEEGGDE FHWHRNVYAP L KYSVAEIF ...String:
MSEFSQTVPE LVAWARKNDF SISLPVDRLS FLLAVATLNG ERLDGEMSEG ELVDAFRHVS DAFEQTSETI GVRANNAIND MVRQRLLNR FTSEQAEGNA IYRLTPLGIG ITDYYIRQRE FSTLRLSMQL SIVAGELKRA ADAAEEGGDE FHWHRNVYAP L KYSVAEIF DSIDLTQRLM DEQQQQVKDD IAQLLNKDWR AAISSCELLL SETSGTLREL QDTLEAAGDK LQANLLRIQD AT MTHDDLH FVDRLVFDLQ SKLDRIISWG QQSIDLWIGY DRHVHKFIRT AIDMDKNRVF AQRLRQSVQT YFDEPWALTY ANA DRLLDM RDEEMALRDE EVTGELPEDL EYEEFNEIRE QLAAIIEEQL AVYKTRQVPL DLGLVVREYL SQYPRARHFD VARI VIDQA VRLGVAQADF TGLPAKWQPI NDYGAKVQAH VIDKY

UniProtKB: Chromosome partition protein MukF

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Macromolecule #2: Chromosome partition protein MukE

MacromoleculeName: Chromosome partition protein MukE / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 27.006484 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSSTNIEQVM PVKLAQALAN PLFPALDSAL RSGRHIGLDE LDNHAFLMDF QEYLEEFYAR YNVELIRAPE GFFYLRPRST TLIPRSVLS ELDMMVGKIL CYLYLSPERL ANEGIFTQQE LYDELLTLAD EAKLLKLVNN RSTGSDVDRQ KLQEKVRSSL N RLRRLGMV ...String:
MSSTNIEQVM PVKLAQALAN PLFPALDSAL RSGRHIGLDE LDNHAFLMDF QEYLEEFYAR YNVELIRAPE GFFYLRPRST TLIPRSVLS ELDMMVGKIL CYLYLSPERL ANEGIFTQQE LYDELLTLAD EAKLLKLVNN RSTGSDVDRQ KLQEKVRSSL N RLRRLGMV WFMGHDSSKF RITESVFRFG ADVRAGDDPR EAQRRLIRDG EAMPIENHLQ LNDETEENQP DSGEEE

UniProtKB: Chromosome partition protein MukE

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Macromolecule #3: Probable RecBCD inhibitor gp5.9

MacromoleculeName: Probable RecBCD inhibitor gp5.9 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T7 (virus)
Molecular weightTheoretical: 6.260819 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
GPGMSRDLVT IPRDVWNDIQ GYIDSLEREN DSLKNQLMEA DEYVAELEEK LNGTS

UniProtKB: Probable RecBCD inhibitor gp5.9

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
GridModel: Quantifoil R2/2 / Material: COPPER/RHODIUM / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: NITROGEN / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 57528
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: OTHER

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

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

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