Crystal structure at 2.0 A of the S-component for thiamin from an ECF-type ABC transporter

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 

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The structural basis of modularity in ECF-type ABC transporters.

Erkens, G.B.Berntsson, R.P.Fulyani, F.Majsnerowska, M.Ter Beek, J.Poolman, B.Slotboom, D.J.

(2011) Nat Struct Mol Biol 18: 755-760

  • DOI: https://doi.org/10.1038/nsmb.2073
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Energy coupling factor (ECF) transporters are used for the uptake of vitamins in Prokarya. They consist of an integral membrane protein that confers substrate specificity (the S-component) and an energizing module that is related to ATP-binding cassette (ABC) transporters. S-components for different substrates often do not share detectable sequence similarity but interact with the same energizing module. Here we present the crystal structure of the thiamine-specific S-component ThiT from Lactococcus lactis at 2.0 Å. Extensive protein-substrate interactions explain its high binding affinity for thiamine (K(d) ~10(-10) M). ThiT has a fold similar to that of the riboflavin-specific S-component RibU, with which it shares only 14% sequence identity. Two alanines in a conserved motif (AxxxA) located on the membrane-embedded surface of the S-components mediate the interaction with the energizing module. Based on these findings, we propose a general transport mechanism for ECF transporters.

  • Organizational Affiliation

    University of Groningen, Groningen Biomolecular Science and Biotechnology Institute, Groningen, The Netherlands.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
192Lactococcus cremoris subsp. cremoris NZ9000Mutation(s): 0 
Gene Names: LLNZ_01755
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on BNG

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B]
nonyl beta-D-glucopyranoside
C15 H30 O6
Query on VIB

Download Ideal Coordinates CCD File 
J [auth A],
O [auth B]
C12 H17 N4 O S
Binding Affinity Annotations 
IDSourceBinding Affinity
VIB Binding MOAD:  3RLB Kd: 0.12 (nM) from 1 assay(s)
PDBBind:  3RLB Kd: 0.12 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.654α = 90
b = 84.654β = 95.81
c = 127.301γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-07-20
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2024-02-28
    Changes: Data collection, Database references, Refinement description, Structure summary