3KCV | pdb_00003kcv

Structure of formate channel


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.260 (Depositor), 0.261 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history

Literature

Structure of the formate transporter FocA reveals a pentameric aquaporin-like channel

Wang, Y.Huang, Y.Wang, J.Cheng, C.Huang, W.Lu, P.Xu, Y.-N.Wang, P.Yan, N.Shi, Y.

(2009) Nature 462: 467-472

  • DOI: https://doi.org/10.1038/nature08610
  • Primary Citation Related Structures: 
    3KCU, 3KCV

  • PubMed Abstract: 

    FocA is a representative member of the formate-nitrite transporter family, which transports short-chain acids in bacteria, archaea, fungi, algae and parasites. The structure and transport mechanism of the formate-nitrite transporter family remain unknown. Here we report the crystal structure of Escherichia coli FocA at 2.25 A resolution. FocA forms a symmetric pentamer, with each protomer consisting of six transmembrane segments. Despite a lack of sequence homology, the overall structure of the FocA protomer closely resembles that of aquaporin and strongly argues that FocA is a channel, rather than a transporter. Structural analysis identifies potentially important channel residues, defines the channel path and reveals two constriction sites. Unlike aquaporin, FocA is impermeable to water but allows the passage of formate. A structural and biochemical investigation provides mechanistic insights into the channel activity of FocA.


  • Organizational Affiliation
    • Ministry of Education Protein Science Laboratory, Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.

Macromolecule Content 

  • Total Structure Weight: 310.13 kDa 
  • Atom Count: 19,120 
  • Modeled Residue Count: 2,510 
  • Deposited Residue Count: 2,850 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable formate transporter 1
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
285Escherichia coli O157:H7Mutation(s): 0 
Gene Names: FOCA
Membrane Entity: Yes 
UniProt
Find proteins for P0AC25 (Escherichia coli O157:H7)
Explore P0AC25 
Go to UniProtKB:  P0AC25
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AC25
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.260 (Depositor), 0.261 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.034α = 90
b = 107.034β = 90
c = 285.452γ = 120
Software Package:
Software NamePurpose
BSSdata collection
PHASERphasing
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-01-22
    Changes: Database references
  • Version 1.3: 2018-02-21
    Changes: Data collection
  • Version 1.4: 2023-11-01
    Changes: Data collection, Database references, Refinement description