4ZIR

Crystal structure of EcfAA' heterodimer bound to AMPPNP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.198 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

ATP binding drives substrate capture in an ECF transporter by a release-and-catch mechanism.

Karpowich, N.K.Song, J.M.Cocco, N.Wang, D.N.

(2015) Nat Struct Mol Biol 22: 565-571

  • DOI: https://doi.org/10.1038/nsmb.3040
  • Primary Citation of Related Structures:  
    4ZIR

  • PubMed Abstract: 

    ECF transporters are a family of active transporters for vitamins. They are composed of four subunits: a membrane-embedded substrate-binding subunit (EcfS), a transmembrane coupling subunit (EcfT) and two ATP-binding-cassette ATPases (EcfA and EcfA'). We have investigated the mechanism of the ECF transporter for riboflavin from the pathogen Listeria monocytogenes, LmECF-RibU. Using structural and biochemical approaches, we found that ATP binding to the EcfAA' ATPases drives a conformational change that dissociates the S subunit from the EcfAA'T ECF module. Upon release from the ECF module, the RibU S subunit then binds the riboflavin transport substrate. We also find that S subunits for distinct substrates compete for the ATP-bound state of the ECF module. Our results explain how ECF transporters capture the transport substrate and reproduce the in vivo observations on S-subunit competition for which the family was named.


  • Organizational Affiliation

    Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, New York, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Energy-coupling factor transporter ATP-binding protein EcfA2267Thermotoga maritima MSB8Mutation(s): 0 
Gene Names: ecfA2ecfAecfA'TM_0222
EC: 3.6.3
UniProt
Find proteins for Q9WY65 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9WY65 
Go to UniProtKB:  Q9WY65
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WY65
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Energy-coupling factor transporter ATP-binding protein EcfA1268Thermotoga maritima MSB8Mutation(s): 7 
Gene Names: ecfA1cbiOecfA'TM_1663
EC: 3.6.3
UniProt
Find proteins for Q9X1Z1 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X1Z1 
Go to UniProtKB:  Q9X1Z1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X1Z1
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.198 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.275α = 90
b = 107.275β = 90
c = 96.758γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL091618

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-10
    Type: Initial release
  • Version 1.1: 2015-06-17
    Changes: Database references
  • Version 1.2: 2015-06-24
    Changes: Database references
  • Version 1.3: 2015-07-22
    Changes: Database references
  • Version 1.4: 2019-11-27
    Changes: Author supporting evidence, Derived calculations, Source and taxonomy
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description