9GBV

E.coli gyrase holocomplex with chirally wrapped 217 bp DNA fragment

• PDB DOI: https://doi.org/10.2210/pdb9GBV/pdb
• EM Map EMD-51222: EMDB EMDataResource
• NAKB: 9GBV

• Classification: ISOMERASE
• Organism(s): Escherichia coli, Escherichia phage Mu
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): No 


• Deposited: 2024-07-31 Released: 2024-08-21 
• Deposition Author(s): Michalczyk, E., Ghilarov, D.
• Funding Organization(s): Wellcome Trust, Biotechnology and Biological Sciences Research Council (BBSRC), Polish National Science Centre

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.32 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of Escherichia coli DNA gyrase with chirally wrapped DNA supports ratchet-and-pawl mechanism for an ATP-powered supercoiling motor

Michalczyk, E., Pakosz-Stepien, Z., Liston, J., Gittins, O., Pabis, M., Heddle, J.G., Ghilarov, D.

(2024) Proceedings Of The National Academy Of Sciences Usa 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 509.25 kDa 
• Atom Count: 31,890 
• Modelled Residue Count: 3,554 
• Deposited Residue Count: 3,810 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit A	A, B [auth C]	880	Escherichia coli	Mutation(s): 0  Gene Names: gyrA, hisW, nalA, parD, b2231, JW2225 EC: 5.6.2.2
UniProt
Find proteins for P0AES4 (Escherichia coli (strain K12)) Explore P0AES4  Go to UniProtKB:  P0AES4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit B	C [auth B], D	811	Escherichia coli	Mutation(s): 0  Gene Names: gyrB, acrB, cou, himB, hisU, nalC, parA, pcbA, b3699, JW5625 EC: 5.6.2.2
UniProt
Find proteins for P0AES6 (Escherichia coli (strain K12)) Explore P0AES6  Go to UniProtKB:  P0AES6

Entity ID: 3
Molecule	Chains	Length	Organism	Image
Mu217 DNA (159-MER)	E	214	Escherichia phage Mu

Entity ID: 4
Molecule	Chains	Length	Organism	Image
Mu217 DNA (159-MER)	F	214	Escherichia phage Mu

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	G [auth D], H [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.32 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	cryoSPARC
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-21 
Deposition Author(s): Michalczyk, E., Ghilarov, D.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	221868/Z/20/Z
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/X01097X/1
Polish National Science Centre	Poland	2020/39/B/NZ1/02898

Revision History  

• Version 1.0: 2024-08-21
  Type: Initial release