3P5N | pdb_00003p5n

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 
    0.289 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.265 (Depositor), 0.270 (DCC) 
  • R-Value Observed: 
    0.266 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1038/nature09488
  • Primary Citation Related Structures: 
    3P5N

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 42.8 kDa 
  • Atom Count: 2,660 
  • Modeled Residue Count: 336 
  • Deposited Residue Count: 378 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Riboflavin uptake protein
A, B
189Staphylococcus aureus subsp. aureus TCH60Mutation(s): 0 
Gene Names: HMPREF0772_2174
Membrane Entity: Yes 
UniProt
Find proteins for E5QVT2 (Staphylococcus aureus (strain TCH60))
Explore E5QVT2 
Go to UniProtKB:  E5QVT2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE5QVT2
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free:  0.289 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.265 (Depositor), 0.270 (DCC) 
  • R-Value Observed: 0.266 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.434α = 90
b = 94.244β = 90
c = 115.402γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references, Derived calculations, Refinement description