9WUS | pdb_00009wus

Cryo-EM Structure of the Periplasmic Domain of AAA Protease FtsH

• PDB DOI: https://doi.org/10.2210/pdb9WUS/pdb
• EM Map EMD-66269: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-09-18 Released: 2026-05-13 
• Deposition Author(s): Kabasakal, B.V., Goc, G., Yadav, S., Borucu, U., Berger, I., Schaffitzel, C.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), Wellcome Trust, Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Cryo-EM Structure of the FtsH Periplasmic Domain Reveals Functional Dynamics.

Goc, G., Yadav, S.K.N., Orriss, G., Borucu, U., Berger, I., Schaffitzel, C., Kabasakal, B.V.

(2026) ACS Chem Biol 21: 844-851

• PubMed: 41944809 
• DOI: https://doi.org/10.1021/acschembio.5c01025
• Primary Citation Related Structures: 
  9WUS


• PubMed Abstract: 
  

  FtsH, an AAA + metalloprotease that is essential in bacteria and eukaryotic organelles, maintains cellular homeostasis by degrading misfolded and membrane-associated proteins. Here, we report cryo-EM structures of the Escherichia coli FtsH periplasmic domain (FtsH-PD) revealing insights into its intrinsic conformational flexibility. Our analysis resolved two distinct states: a 4.9 Å structure exhibiting the conserved α + β fold and a 7.3 Å map representing distinct rotated-helix conformation characterized by 20° clockwise rotation of two alpha helices. These findings support a model where conformational changes are present not only in the FtsH cytosolic domain but also in the periplasmic domain. This flexibility potentially facilitates substrate translocation through a combination of mechanisms involving both the FtsH-PD and the HflKC complexed with FtsH, along with lipid-scramblase activity, to assist in membrane protein extraction. This study offers new perspectives on how conformational changes in the periplasmic domain contribute to FtsH substrate degradation mechanisms.

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Organizational Affiliation: 
• Turkish Accelerator and Radiation Laboratory, Ankara 06830, Türkiye.
Department of Biology, Kocaeli University, Kocaeli 41001, Türkiye.
School of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K.
School of Chemistry and Max Planck Bristol Centre for Minimal Biology, University of Bristol, Bristol BS8 1TH, U.K.
Department of Biological Sciences, Middle East Technical University, Ankara 06800, Türkiye.

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 45.07 kDa 
• Atom Count: 3,168 
• Modeled Residue Count: 390 
• Deposited Residue Count: 390 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent zinc metalloprotease FtsH	A, B, C, D, E, F	65	Escherichia coli	Mutation(s): 0  Gene Names: ftsH, hflB, mrsC, std, tolZ, b3178, JW3145 EC: 3.4.24
UniProt
Find proteins for P0AAI3 (Escherichia coli (strain K12)) Explore P0AAI3  Go to UniProtKB:  P0AAI3

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-05-13 
Deposition Author(s): Kabasakal, B.V., Goc, G., Yadav, S., Borucu, U., Berger, I., Schaffitzel, C.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/P000940/1
Wellcome Trust	United Kingdom	210701/Z/18/Z
Other government	Turkey	TUBITAK - 118C225

Revision History  

• Version 1.0: 2026-05-13
  Type: Initial release