3P5N

Structure and mechanism of the S component of a bacterial ECF transporter


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.265 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and mechanism of the S component of a bacterial ECF transporter

Zhang, P.Wang, J.Shi, Y.

(2010) Nature 468: 717-720

  • DOI: 10.1038/nature09488

  • PubMed Abstract: 
  • The energy-coupling factor (ECF) transporters, responsible for vitamin uptake in prokaryotes, are a unique family of membrane transporters. Each ECF transporter contains a membrane-embedded, substrate-binding protein (known as the S component), an en ...

    The energy-coupling factor (ECF) transporters, responsible for vitamin uptake in prokaryotes, are a unique family of membrane transporters. Each ECF transporter contains a membrane-embedded, substrate-binding protein (known as the S component), an energy-coupling module that comprises two ATP-binding proteins (known as the A and A' components) and a transmembrane protein (known as the T component). The structure and transport mechanism of the ECF family remain unknown. Here we report the crystal structure of RibU, the S component of the ECF-type riboflavin transporter from Staphylococcus aureus at 3.6-Å resolution. RibU contains six transmembrane segments, adopts a previously unreported transporter fold and contains a riboflavin molecule bound to the L1 loop and the periplasmic portion of transmembrane segments 4-6. Structural analysis reveals the essential ligand-binding residues, identifies the putative transport path and, with sequence alignment, uncovers conserved structural features and suggests potential mechanisms of action among the ECF transporters.


    Organizational Affiliation

    Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, New Jersey 08544, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Riboflavin uptake protein
A, B
189Staphylococcus aureus (strain TCH60)Mutation(s): 0 
Gene Names: ribU
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Energy-Coupling Factor (ECF) Transporters
Protein: 
RibU, S Component of the Riboflavin Transporter
Find proteins for E5QVT2 (Staphylococcus aureus (strain TCH60))
Go to UniProtKB:  E5QVT2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RBF
Query on RBF

Download SDF File 
Download CCD File 
A, B
RIBOFLAVIN
RIBOFLAVINE; VITAMIN B2
C17 H20 N4 O6
AUNGANRZJHBGPY-SCRDCRAPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.265 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.434α = 90.00
b = 94.244β = 90.00
c = 115.402γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXphasing
PHENIXrefinement
HKL-2000data reduction
DENZOdata reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-11-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description