7NZ2

Cryo-EM structure of the MukBEF-MatP-DNA tetrad


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/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. 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.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chromosome partition protein MukB1,482Photorhabdus thracensisMutation(s): 1 
Gene Names: mukBVY86_15870
UniProt
Find proteins for A0A0F7LRY2 (Photorhabdus thracensis)
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Go to UniProtKB:  A0A0F7LRY2
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UniProt GroupA0A0F7LRY2
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Chromosome partition protein MukFI [auth C1],
J [auth C2],
K [auth D1],
L [auth D2]
440Photorhabdus thracensisMutation(s): 0 
Gene Names: mukFVY86_15860
UniProt
Find proteins for A0A0F7LMQ4 (Photorhabdus thracensis)
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UniProt GroupA0A0F7LMQ4
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Chromosome partition protein MukE240Photorhabdus thracensisMutation(s): 0 
Gene Names: mukEVY86_15865
UniProt
Find proteins for A0A0F7LPV6 (Photorhabdus thracensis)
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UniProt GroupA0A0F7LPV6
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein78Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Macrodomain Ter protein151Photorhabdus thracensisMutation(s): 0 
Gene Names: matPVY86_22090
UniProt
Find proteins for A0A0F7LUV5 (Photorhabdus thracensis)
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UniProt GroupA0A0F7LUV5
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Entity ID: 6
MoleculeChains LengthOrganismImage
matS2 DNA 80 b, oligo FBA769KA [auth K1],
LA [auth K2],
QA [auth N1],
RA [auth N2]
80Photorhabdus thracensis
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Entity ID: 7
MoleculeChains LengthOrganismImage
matS2 DNA 80 b, oligo FBA770MA [auth L1],
NA [auth L2],
OA [auth M1],
PA [auth M2]
80Photorhabdus thracensis
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
BB [auth B1]
DB [auth B2]
EB [auth B3]
GB [auth B4]
TA [auth A1]
BB [auth B1],
DB [auth B2],
EB [auth B3],
GB [auth B4],
TA [auth A1],
UA [auth A2],
WA [auth A3],
ZA [auth A4]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
PNS
Query on PNS

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IB [auth G1]
JB [auth G2]
KB [auth G3]
LB [auth G4]
MB [auth H1]
IB [auth G1],
JB [auth G2],
KB [auth G3],
LB [auth G4],
MB [auth H1],
NB [auth H2],
OB [auth H3],
PB [auth H4]
4'-PHOSPHOPANTETHEINE
C11 H23 N2 O7 P S
JDMUPRLRUUMCTL-VIFPVBQESA-N
MG
Query on MG

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AB [auth B1]
CB [auth B2]
FB [auth B3]
HB [auth B4]
SA [auth A1]
AB [auth B1],
CB [auth B2],
FB [auth B3],
HB [auth B4],
SA [auth A1],
VA [auth A2],
XA [auth A3],
YA [auth A4]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.0 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
  • Version 1.2: 2022-06-29
    Changes: Database references