9I3K | pdb_00009i3k

Asymmetric cryo-EM reconstruction of the full-length E. coli transmembrane formate transporter FocA

• PDB DOI: https://doi.org/10.2210/pdb9I3K/pdb
• EM Map EMD-52595: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2025-01-23 Released: 2025-10-22 
• Deposition Author(s): Tueting, C., Janson, K., Kyrilis, F.L., Hamdi, F., Kastritis, P.L.
• Funding Organization(s): German Federal Ministry for Education and Research, German Research Foundation (DFG), European Regional Development Fund, European Research Council (ERC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.87 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Conserved hydrophilic checkpoints tune FocA-mediated formate:H + symport.

Tuting, C., Janson, K., Kammel, M., Ihling, C., Lorenz, J., Kyrilis, F.L., Hamdi, F., Erdmann, C., Sinz, A., Sawers, R.G., Kastritis, P.L.

(2025) Nat Commun 16: 9476-9476

• PubMed: 41145500 
• DOI: https://doi.org/10.1038/s41467-025-65159-3
• Primary Citation of Related Structures:  
  9G49, 9G4D, 9I3K


• PubMed Abstract: 
  

  FocA belongs to the widespread, evolutionarily ancient formate-nitrite transporter (FNT) family of pentameric anion channels and translocates formic acid bidirectionally. Here, we identify compartmentalized polarity distribution across the complete FocA pore structure - resolved at 2.56 Å - mirrored against a two-fold axis with H209 at its center. A FocA-H209N variant that exhibits an efflux-only channel-like function in vivo reveals a density consistent with formate located directly at N209, abolishing the channel's amphiphilicity. Pyruvate formate-lyase, which generates formate, orients at the cytoplasmic face where formate delivery is regulated by conformational changes in the FocA vestibule. Comparisons with other FNTs suggest a tuning mechanism of formate-specific transport via checkpoints enriched in hydrophilic residues.

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Organizational Affiliation: 
• Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle (Saale), Germany.
Department of Integrative Structural Biochemistry, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Weinbergweg 22, Halle (Saale), Germany.
Institute of Biology / Microbiology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle (Saale), Germany.
Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle (Saale), Germany.
Center for Structural Mass Spectrometry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle (Saale), Germany.
Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece.
Institute of Biology / Microbiology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle (Saale), Germany. [e-mail].
Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle (Saale), Germany. [e-mail].
Department of Integrative Structural Biochemistry, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Weinbergweg 22, Halle (Saale), Germany. [e-mail].
Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece. [e-mail].
Biozentrum, Martin Luther University Halle-Wittenberg, Weinbergweg 22, Halle (Saale), Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 155.06 kDa 
• Atom Count: 10,350 
• Modeled Residue Count: 1,360 
• Deposited Residue Count: 1,425 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formate channel FocA	A, B, C, D, E	285	Escherichia coli K-12	Mutation(s): 0  Gene Names: focA, ycaE, b0904, JW0887
UniProt
Find proteins for P0AC23 (Escherichia coli (strain K12)) Explore P0AC23  Go to UniProtKB:  P0AC23

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.87 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Coot	0.9.6
MODEL REFINEMENT	PHENIX	1.12rc1
RECONSTRUCTION	cryoSPARC	4.4

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-22 
Deposition Author(s): Tueting, C., Janson, K., Kyrilis, F.L., Hamdi, F., Kastritis, P.L.

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Funding Organization	Location	Grant Number
German Federal Ministry for Education and Research	Germany	03Z22HN23
German Federal Ministry for Education and Research	Germany	03Z22HI2
German Federal Ministry for Education and Research	Germany	03COV04
German Research Foundation (DFG)	Germany	391498659
European Regional Development Fund	European Union	EFRE: ZS/2016/04/78115
European Research Council (ERC)	European Union	101086665

Revision History  

• Version 1.0: 2025-10-22
  Type: Initial release
  
• Version 1.1: 2025-11-05
  Changes: Data collection, Database references