7NYX

Cryo-EM structure of the MukBEF-MatP-DNA monomer (closed conformation)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Cryo-EM structure of MukBEF reveals DNA loop entrapment at chromosomal unloading sites.

Burmann, F., Funke, L.F.H., Chin, J.W., Lowe, J.

(2021) Mol Cell 81: 4891-4906.e8

  • DOI: 10.1016/j.molcel.2021.10.011
  • Primary Citation of Related Structures:  
    7NYW, 7NYX, 7NYY, 7NYZ, 7NZ0, 7NZ2, 7NZ3, 7NZ4

  • PubMed 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 activity within the replication terminus macrodomain is suppressed by the sequence-specific unloader MatP ...

    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.

    Related Citations: 
    • DNA entrapment revealed by the structure of bacterial condensin MukBEF
      Buermann, F., Funke, L.F.H., Chin, J.W., Lowe, J.
      (2021) Biorxiv --: --
    Organizational Affiliation: 

    MRC Laboratory of Molecular Biology, Structural Studies Division, Cambridge Biomedical Campus, Cambridge, UK. Electronic address: jyl@mrc-lmb.cam.ac.uk.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Chromosome partition protein MukBA, B1,482Photorhabdus thracensisMutation(s): 1 
Gene Names: mukB, VY86_15870
UniProt
Find proteins for A0A0F7LRY2 (Photorhabdus thracensis)
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UniProt GroupA0A0F7LRY2
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Chromosome partition protein MukFC, D440Photorhabdus thracensisMutation(s): 0 
Gene Names: mukF, VY86_15860
UniProt
Find proteins for A0A0F7LMQ4 (Photorhabdus thracensis)
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UniProt GroupA0A0F7LMQ4
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Chromosome partition protein MukEE, F240Photorhabdus thracensisMutation(s): 0 
Gene Names: mukE, VY86_15865
UniProt
Find proteins for A0A0F7LPV6 (Photorhabdus thracensis)
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UniProt GroupA0A0F7LPV6
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Acyl carrier proteinG, H78Escherichia coli BL21(DE3)Mutation(s): 0 
UniProt
Find proteins for P0A6A8 (Escherichia coli (strain K12))
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UniProt GroupP0A6A8
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Macrodomain Ter proteinI, J151Photorhabdus thracensisMutation(s): 0 
Gene Names: matP, VY86_22090
UniProt
Find proteins for A0A0F7LUV5 (Photorhabdus thracensis)
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UniProt GroupA0A0F7LUV5
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Entity ID: 6
MoleculeChainsLengthOrganismImage
matS2 DNA 80 b, oligo FBA769K80synthetic construct
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Entity ID: 7
MoleculeChainsLengthOrganismImage
matS2 DNA 80 b, oligo FBA770L80synthetic construct
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Entity ID: 8
MoleculeChainsLengthOrganismImage
DNA 80 bM, N30synthetic construct
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP
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P [auth A],
Q [auth B]		ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N		 Ligand Interaction
PNS
Query on PNS
Download Ideal Coordinates CCD File 
S [auth G],
T [auth H]		4'-PHOSPHOPANTETHEINE
C11 H23 N2 O7 P S
JDMUPRLRUUMCTL-VIFPVBQESA-N		 Ligand Interaction
MG
Query on MG
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O [auth A],
R [auth B]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-07
    Type: Initial release
  • Version 1.1: 2022-03-23
    Changes: Database references, Source and taxonomy, Structure summary