9N2E | pdb_00009n2e

Cryo-EM structure of F. johnsoniae BamAP

• PDB DOI: https://doi.org/10.2210/pdb9N2E/pdb
• EM Map EMD-48836: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Flavobacterium johnsoniae UW101
• Mutation(s): No 
• Membrane Protein: Yes  MemProtMD


• Deposited: 2025-01-28 Released: 2025-07-09 
• Deposition Author(s): Deme, J.C., Lea, S.M.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

A shared mechanism for Bacteroidota protein transport and gliding motility.

Liu, X., Avramova, M., Deme, J.C., Jones, R.L., Lundgren, C.A.K., Lea, S.M., Berks, B.C.

(2025) Nat Commun 16: 10217-10217

• PubMed: 41266322 
• DOI: https://doi.org/10.1038/s41467-025-65003-8
• Primary Citation of Related Structures:  
  9N2D, 9N2E


• PubMed Abstract: 
  

  Bacteria of the phylum Bacteroidota are major human commensals and pathogens in addition to being abundant members of the wider biosphere. Bacteroidota move by gliding and they export proteins using the Type 9 Secretion System (T9SS). Here we discover that gliding motility and the T9SS share an unprecedented mechanism of energisation in which outer membrane proteins are covalently attached by disulfide bonds to a moving internal track structure that propels them laterally through the membrane. We determined the structure of an exemplar Bacteroidota mobile track by obtaining the cryoEM structure of a 3 MDa circular mini-track from Porphyromonas gingivalis. Our discoveries identify a mechanistic and evolutionary link between gliding motility and T9SS-dependent protein transport.

---

Organizational Affiliation: 
• Department of Biochemistry, University of Oxford, Oxford, UK. [e-mail].
Department of Biochemistry, University of Oxford, Oxford, UK.
Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA. [e-mail].
Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA. [e-mail].
Department of Biochemistry, University of Oxford, Oxford, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 129.9 kDa 
• Atom Count: 4,928 
• Modeled Residue Count: 613 
• Deposited Residue Count: 1,149 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Surface antigen (D15)	A	900	Flavobacterium johnsoniae UW101	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A5FJ90 (Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / JCM 8514 / BCRC 14874 / CCUG 350202 / NBRC 14942 / NCIMB 11054 / UW101)) Explore A5FJ90  Go to UniProtKB:  A5FJ90

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CarboxypepD_reg-like domain-containing protein	B [auth E]	249	Flavobacterium johnsoniae UW101	Mutation(s): 0
UniProt
Find proteins for A5FJ21 (Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / JCM 8514 / BCRC 14874 / CCUG 350202 / NBRC 14942 / NCIMB 11054 / UW101)) Explore A5FJ21  Go to UniProtKB:  A5FJ21

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	dev_5533

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-09 
Deposition Author(s): Deme, J.C., Lea, S.M.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CCR Core Funding for Lea Group

Revision History  

• Version 1.0: 2025-07-09
  Type: Initial release
  
• Version 1.1: 2026-01-21
  Changes: Data collection, Database references, Structure summary