9GM8 | pdb_00009gm8

MukBEF in a nucleotide-bound state with open neck gate

• PDB DOI: https://doi.org/10.2210/pdb9GM8/pdb
• EM Map EMD-51444: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN
• Organism(s): Photorhabdus thracensis, Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-08-28 Released: 2025-03-26 
• Deposition Author(s): Burmann, F., Lowe, J.
• Funding Organization(s): European Molecular Biology Organization (EMBO)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for DNA capture by the MukBEF SMC complex and its inhibition by a viral DNA mimic

Burmann, F., Dillingham, M., Lowe, F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 8-mer - A2B2C2D1E1 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 514.75 kDa 
• Atom Count: 28,574 
• Modelled Residue Count: 3,541 
• Deposited Residue Count: 4,480 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromosome partition protein MukF	A [auth C], H [auth D]	440	Photorhabdus thracensis	Mutation(s): 0  Gene Names: mukF, VY86_15860
UniProt
Find proteins for A0A0F7LMQ4 (Photorhabdus thracensis) Explore A0A0F7LMQ4  Go to UniProtKB:  A0A0F7LMQ4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromosome partition protein MukE	B [auth E], C [auth F]	240	Photorhabdus thracensis	Mutation(s): 0  Gene Names: mukE, VY86_15865
UniProt
Find proteins for A0A0F7LPV6 (Photorhabdus thracensis) Explore A0A0F7LPV6  Go to UniProtKB:  A0A0F7LPV6

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl carrier protein	D [auth G], E [auth I]	78	Escherichia coli	Mutation(s): 0  Gene Names: acpP, b1094, JW1080
UniProt
Find proteins for P0A6A8 (Escherichia coli (strain K12)) Explore P0A6A8  Go to UniProtKB:  P0A6A8

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromosome partition protein MukB	F [auth A], G [auth B]	1,482	Photorhabdus thracensis	Mutation(s): 0  Gene Names: mukB, VY86_15870
UniProt
Find proteins for A0A0F7LRY2 (Photorhabdus thracensis) Explore A0A0F7LRY2  Go to UniProtKB:  A0A0F7LRY2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP (Subject of Investigation/LOI)	J [auth A], L [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)	I [auth A], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
4HH	D [auth G], E [auth I]	L-PEPTIDE LINKING	C14 H28 N3 O9 P S		SER

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-26 
Deposition Author(s): Burmann, F., Lowe, J.

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Funding Organization	Location	Grant Number
European Molecular Biology Organization (EMBO)	European Union	ALTF 605-2019

Revision History  

• Version 1.0: 2025-03-26
  Type: Initial release