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- PDB-7nz2: Cryo-EM structure of the MukBEF-MatP-DNA tetrad -

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Basic information

Entry
Database: PDB / ID: 7nz2
TitleCryo-EM structure of the MukBEF-MatP-DNA tetrad
Components
  • (Chromosome partition protein ...) x 3
  • (matS2 DNA 80 b, oligo ...) x 2
  • Acyl carrier protein
  • Macrodomain Ter protein
KeywordsDNA BINDING PROTEIN / SMC-kleisin complex / ATPase
Function / homology
Function and homology information


nucleoid / chromosome condensation / acyl carrier activity / chromosome segregation / DNA replication / sequence-specific DNA binding / cell cycle / cell division / calcium ion binding / regulation of DNA-templated transcription ...nucleoid / chromosome condensation / acyl carrier activity / chromosome segregation / DNA replication / sequence-specific DNA binding / cell cycle / cell division / calcium ion binding / regulation of DNA-templated transcription / DNA binding / ATP binding / cytoplasm
Similarity search - Function
Macrodomain Ter protein, MatP / MatP, N-terminal / MatP, C-terminal ribbon-helix-helix domain / MatP, N-terminal domain superfamily / MatP N-terminal domain / MatP C-terminal ribbon-helix-helix domain / Prokaryotic chromosome segregation/condensation protein MukE / MukE, C-terminal domain / MukE, N-terminal domain / MukE-like family ...Macrodomain Ter protein, MatP / MatP, N-terminal / MatP, C-terminal ribbon-helix-helix domain / MatP, N-terminal domain superfamily / MatP N-terminal domain / MatP C-terminal ribbon-helix-helix domain / 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 / MukB, N-terminal domain / Chromosome partition protein MukB / MukB, hinge domain / MukB, hinge domain superfamily / MukB N-terminal / MukB hinge domain / SbcC/RAD50-like, Walker B motif / Arc-type ribbon-helix-helix / 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 / 4'-PHOSPHOPANTETHEINE / DNA / DNA (> 10) / Chromosome partition protein MukF / Chromosome partition protein MukE / Chromosome partition protein MukB / Macrodomain Ter protein / Acyl carrier protein
Similarity search - Component
Biological speciesPhotorhabdus thracensis (bacteria)
Escherichia coli BL21 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 11 Å
AuthorsBuermann, F. / Lowe, J.
Citation
Journal: Mol Cell / Year: 2021
Title: Cryo-EM structure of MukBEF reveals DNA loop entrapment at chromosomal unloading sites.
Authors: Frank Bürmann / Louise F H Funke / Jason W Chin / Jan Löwe /
Abstract: The ring-like structural maintenance of chromosomes (SMC) complex MukBEF folds the genome of Escherichia coli and related bacteria into large loops, presumably by active DNA loop extrusion. MukBEF ...The ring-like structural maintenance of chromosomes (SMC) complex MukBEF folds the genome of Escherichia coli and related bacteria into large loops, presumably by active DNA loop extrusion. MukBEF activity within the replication terminus macrodomain is suppressed by the sequence-specific unloader MatP. Here, we present the complete atomic structure of MukBEF in complex with MatP and DNA as determined by electron cryomicroscopy (cryo-EM). The complex binds two distinct DNA double helices corresponding to the arms of a plectonemic loop. MatP-bound DNA threads through the MukBEF ring, while the second DNA is clamped by the kleisin MukF, MukE, and the MukB ATPase heads. Combinatorial cysteine cross-linking confirms this topology of DNA loop entrapment in vivo. Our findings illuminate how a class of near-ubiquitous DNA organizers with important roles in genome maintenance interacts with the bacterial chromosome.
#1: Journal: Biorxiv / Year: 2021
Title: DNA entrapment revealed by the structure of bacterial condensin MukBEF
Authors: Buermann, F. / Funke, L.F.H. / Chin, J.W. / Lowe, J.
History
DepositionMar 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Source and taxonomy / Structure summary
Category: database_2 / em_entity_assembly ...database_2 / em_entity_assembly / em_entity_assembly_naturalsource / em_entity_assembly_recombinant
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 29, 2022Group: Database references / Category: citation / citation_author

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Structure visualization

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  • EMDB-12662
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Assembly

Deposited unit
A1: Chromosome partition protein MukB
A2: Chromosome partition protein MukB
A3: Chromosome partition protein MukB
A4: Chromosome partition protein MukB
B1: Chromosome partition protein MukB
B2: Chromosome partition protein MukB
B3: Chromosome partition protein MukB
B4: Chromosome partition protein MukB
C1: Chromosome partition protein MukF
C2: Chromosome partition protein MukF
D1: Chromosome partition protein MukF
D2: Chromosome partition protein MukF
E1: Chromosome partition protein MukE
E2: Chromosome partition protein MukE
E3: Chromosome partition protein MukE
E4: Chromosome partition protein MukE
F1: Chromosome partition protein MukE
F2: Chromosome partition protein MukE
F3: Chromosome partition protein MukE
F4: Chromosome partition protein MukE
G1: Acyl carrier protein
G2: Acyl carrier protein
G3: Acyl carrier protein
G4: Acyl carrier protein
H1: Acyl carrier protein
H2: Acyl carrier protein
H3: Acyl carrier protein
H4: Acyl carrier protein
I1: Macrodomain Ter protein
I2: Macrodomain Ter protein
I3: Macrodomain Ter protein
I4: Macrodomain Ter protein
J1: Macrodomain Ter protein
J2: Macrodomain Ter protein
J3: Macrodomain Ter protein
J4: Macrodomain Ter protein
K1: matS2 DNA 80 b, oligo FBA769
K2: matS2 DNA 80 b, oligo FBA769
L1: matS2 DNA 80 b, oligo FBA770
L2: matS2 DNA 80 b, oligo FBA770
M1: matS2 DNA 80 b, oligo FBA770
M2: matS2 DNA 80 b, oligo FBA770
N1: matS2 DNA 80 b, oligo FBA769
N2: matS2 DNA 80 b, oligo FBA769
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,199,99568
Polymers2,192,87644
Non-polymers7,11924
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Chromosome partition protein ... , 3 types, 20 molecules A1A2A3A4B1B2B3B4C1C2D1D2E1E2E3E4F1F2F3F4

#1: Protein
Chromosome partition protein MukB / Structural maintenance of chromosome-related protein


Mass: 170240.188 Da / Num. of mol.: 8 / Mutation: E1407Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus thracensis (bacteria) / Gene: mukB, VY86_15870 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F7LRY2
#2: Protein
Chromosome partition protein MukF


Mass: 50193.305 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus thracensis (bacteria) / Gene: mukF, VY86_15860 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F7LMQ4
#3: Protein
Chromosome partition protein MukE


Mass: 27423.848 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus thracensis (bacteria) / Gene: mukE, VY86_15865 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F7LPV6

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Protein , 2 types, 16 molecules G1G2G3G4H1H2H3H4I1I2I3I4J1J2J3J4

#4: Protein
Acyl carrier protein / / ACP


Mass: 8645.460 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6D2XA84
#5: Protein
Macrodomain Ter protein


Mass: 18032.613 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus thracensis (bacteria) / Gene: matP, VY86_22090 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F7LUV5

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MatS2 DNA 80 b, oligo ... , 2 types, 8 molecules K1K2N1N2L1L2M1M2

#6: DNA chain
matS2 DNA 80 b, oligo FBA769


Mass: 24625.713 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Synthetic DNA sequence / Source: (synth.) Photorhabdus thracensis (bacteria)
#7: DNA chain
matS2 DNA 80 b, oligo FBA770


Mass: 24715.855 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Synthetic DNA sequence / Source: (synth.) Photorhabdus thracensis (bacteria)

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Non-polymers , 3 types, 24 molecules

#8: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#9: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#10: Chemical
ChemComp-PNS / 4'-PHOSPHOPANTETHEINE / Phosphopantetheine


Mass: 358.348 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C11H23N2O7PS

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Details

Has ligand of interestN

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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

Component
IDNameTypeEntity IDParent-IDSource
1Complex of MukBEF, AcpP, MatP and DNACOMPLEX#1-#70MULTIPLE SOURCES
2Complex of MukBEFand MatPCOMPLEX#1-#3, #51RECOMBINANT
3Acyl carrier proteinCOMPLEX#41NATURAL
4DNACOMPLEX#6-#71MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Photorhabdus thracensis (bacteria)230089
23Escherichia coli BL21(DE3) (bacteria)469008
34Photorhabdus thracensis (bacteria)230089
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli BL21(DE3) (bacteria)469008
24synthetic construct (others)32630
Buffer solutionpH: 7.3
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

Software
NameVersionClassificationNB
ISOLDE1.1.0model building
UCSF ChimeraX1.1/v9model building
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12010 / Symmetry type: POINT

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