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- EMDB-51443: MukBEF in a nucleotide-bound state with open neck gate (monomer) -

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Basic information

Entry
Database: EMDB / ID: EMD-51443
TitleMukBEF in a nucleotide-bound state with open neck gate (monomer)
Map dataPrimary map
Sample
  • Complex: MukBEF DNA loading reaction
    • Protein or peptide: Chromosome partition protein MukF
    • Protein or peptide: Chromosome partition protein MukE
    • Protein or peptide: Acyl carrier protein
    • Protein or peptide: Chromosome partition protein MukB
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsSMC complex / Chromosome segregation / ABC-type ATPase / DNA BINDING PROTEIN
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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsBurmann F / Lowe J
Funding supportEuropean Union, 1 items
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, 2024-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51443.png

Downloads & links

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Map

FileDownload / File: emd_51443.map.gz / Format: CCP4 / Size: 115.9 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.)
1.48 Å/pix.
x 312 pix.
= 460.98 Å		1.48 Å/pix.
x 312 pix.
= 460.98 Å		1.48 Å/pix.
x 312 pix.
= 460.98 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4775 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.01716789 - 0.04395475
Average (Standard dev.)0.00012269848 (±0.0012964978)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions312312312
Spacing312312312
CellA=B=C: 460.97998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: cryoSPARC noflex map

Fileemd_51443_additional_1.map
AnnotationcryoSPARC noflex map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1

Fileemd_51443_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_51443_half_map_2.map
AnnotationHalf-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : MukBEF DNA loading reaction

EntireName: MukBEF DNA loading reaction
Components
  • Complex: MukBEF DNA loading reaction
    • Protein or peptide: Chromosome partition protein MukF
    • Protein or peptide: Chromosome partition protein MukE
    • Protein or peptide: Acyl carrier protein
    • Protein or peptide: Chromosome partition protein MukB
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: MukBEF DNA loading reaction

SupramoleculeName: MukBEF DNA loading reaction / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Photorhabdus thracensis (bacteria)
Molecular weightTheoretical: 924.253 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: Photorhabdus thracensis (bacteria)
Molecular weightTheoretical: 50.193305 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSEYSQTVPE LVSWARKNDF SISLPVERLA FLMAIAVLNS ERLDGEMSEG ELIDAFREVC KGFEQTAESV AVRANNAIND MVRQKLLNR FTSELADGNA IYRLTPLGIS ISDYYIRQRE FSTLRLSMQL SIVANELHRA AEAAEEGGDE FHWHRNVFAP L KYSVAEIF ...String:
MSEYSQTVPE LVSWARKNDF SISLPVERLA FLMAIAVLNS ERLDGEMSEG ELIDAFREVC KGFEQTAESV AVRANNAIND MVRQKLLNR FTSELADGNA IYRLTPLGIS ISDYYIRQRE FSTLRLSMQL SIVANELHRA AEAAEEGGDE FHWHRNVFAP L KYSVAEIF DSIDMSQRLM DEQQNFVKED IAALLNQDWQ AAIANCEQLL SETSGTLREL QDTLEAAGDK LQANLLRIQD AN MGSGGSE LVDKLVFDLQ SKLDRIISWG QQAIDLWIGY DRHVHKFIRT AIDMDKNRIF SQRLRQSVQH YFDNPWTLTV ANA ERLLDM RDEELALRNE EVTGELPLEL EYEEFSEIND QLAAMIEKAL LVYQQEQRPL DLGAVLRDYL AQHPLPRHFD VARI LVDQA VRLGVAEADF SGLPAEWLAI NDYGAKVQAH VIDTY

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: Photorhabdus thracensis (bacteria)
Molecular weightTheoretical: 27.423848 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSSTHIEQFM PVKLAQALAN SLFPELDSQL RAGRHIGIDD LDNHAFLMDF QEQLEEFYAR YNVELIRAPE GFFYLRPRST TLIPRSVLS ELDMMVGKIL CYLYLSPERL ANQGIFTSQE LYEELISLAD EGKLMKFVNQ RSSGSDLDKQ KLQEKVRTTL N RLRRLGMV ...String:
MSSTHIEQFM PVKLAQALAN SLFPELDSQL RAGRHIGIDD LDNHAFLMDF QEQLEEFYAR YNVELIRAPE GFFYLRPRST TLIPRSVLS ELDMMVGKIL CYLYLSPERL ANQGIFTSQE LYEELISLAD EGKLMKFVNQ RSSGSDLDKQ KLQEKVRTTL N RLRRLGMV YFLPNNNNKF TITEAVFRFG ADVRSGDDPR EIQLRMIRDG EAMPVEGSLS LDDSENDETP DNSAEGAGDE QP

UniProtKB: Chromosome partition protein MukE

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Macromolecule #3: Acyl carrier protein

MacromoleculeName: Acyl carrier protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 8.985794 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSTIEERVKK IIGEQLGVKQ EEVTNNASFV EDLGAD(4HH)LDT VELVMALEEE FDTEIPDEEA EKITTVQAAI DYINGH QA

UniProtKB: Acyl carrier protein

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Macromolecule #4: Chromosome partition protein MukB

MacromoleculeName: Chromosome partition protein MukB / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus thracensis (bacteria)
Molecular weightTheoretical: 170.241172 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIERGKFRSL TLVNWNGFFA RTFDLDELVT TLSGGNGAGK STTMAAFVTA LIPDLTLLHF RNTTEAGATS GSRDKGLHGK LRAGVCYST LDVINSRHQR VVVGVRLQQV AGRDRKVDIK PFMIQGLPTA IQPTQLLTEN VGERQARVLP LNELKDRLDE M EGVQFKQF ...String:
MIERGKFRSL TLVNWNGFFA RTFDLDELVT TLSGGNGAGK STTMAAFVTA LIPDLTLLHF RNTTEAGATS GSRDKGLHGK LRAGVCYST LDVINSRHQR VVVGVRLQQV AGRDRKVDIK PFMIQGLPTA IQPTQLLTEN VGERQARVLP LNELKDRLDE M EGVQFKQF NSITDYHAQM FDLGVIPKRL RSASDRSKFY RLIEASLYGG ISSAITRSLR DYLLPENSGV RKAFQDMEAA LR ENRITLE AIRVTQSDRD LFKHLITEAT SYVSADYMRH ANERRTHLDE ALALRGELFG SHKQLATEQY RHVEMARELA EQS GASSDL ETDHQAASDH LNLVQTAMRQ QEKIDRYQVD LEELSYRLEE QTDVVEEAGE LQAEYEARTE ATEQEVDELK SQLA DYQQA LDVQQTRAIQ YQQALQALER ARELCRLPDL SVDNAEEWLE TFQAKEQQAT EALLALEQKL SVADAAHNQF EQAYQ LVKN IVGETSRSEA WQSARELLRD WPSQRHLADR VQPLRMRLSE LEQRLNNQQN AERLLSEFCK RQGRQYQAED LEALQN ELE ARQEALSLSV NEGGERRMEM RQELEQLKQK IQSLTARAPV WLAAQDTLNQ LCEQSGETLA SSNDVTEYMQ QLLERER EA TVERDEVAAQ KRELEKQIER LSQPSGAEDS RMIALAERFG GVLLSEIYDD ITIDDAPYFS ALYGPARHGI VVPDLSLV R PHLETLEDCP EDLYLIEGDP QSFDDSVFNA EEQTNAVLVK SSDRQWRYSR YPELPLFGRA ARENRLEALN LERDALAER YATLSFDVQK IQRAHQAFSQ FVGKHLSVAF DTDPEAEIRE LRQRHTELER EVSRFEDQTQ QQRQQYAQAK ESLTTLNRLI PQVTLLLDE TLIDRVEEVR EEMDEAQEAA RFLQQHGSAL TKLEPMVAVL QSDPQQHEQL QQDYETAKHS QHQAKQQAFA L VEIVQRRV HFSYSDSAGM LSENADLNDK LRQRLEHAES DRSRAREQLR QQQAQYSQFN QVLASLKSSY ETKQDMLKEL LQ EMKDIGV QADANAEMRA RERRDRLHEA LSVNRSRVNQ LEKQIAFCEA EMENVQKKLR KLERDYYQIR EQVVSAKAGW CAV MRMVKD NGVERRLHRR ELAYMEGGAL RSMSDKALGA LRLAVADNEH LRDALRLSED PKRPERKVQF FIAVYQHLRE RIRQ DIIRT DDPVDAIEQM EIELARLTEE LTAREQKLAI SSKSVANIIR KTIQREQNRI RMLNQGLQAV SFGQVRGVRL NVNVR ESHA ILLDVLSEQQ EQHQDLFNSQ RLTFSEAMAK LYQRLNPQVD MGQRLPQTIG EELLDYRNYL ELDVEVNRGS DGWLKA ESG ALSTGEAIGT GMSILVMVVQ SWEEESRRLR GKDISPCRLL FLDEAARLDA KSIATLFELC ERLQMQLIIA APENISP EK GTTYKLVRKV FKNHEHVHVV GLRGFGQDAP ATQLISDVTA

UniProtKB: Chromosome partition protein MukB

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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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: UltrAuFoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: GOLD / 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Software - details: 3DFlex / Number images used: 34436
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-9gm7:
MukBEF in a nucleotide-bound state with open neck gate (monomer)

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