Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

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This is version 1.3 of the entry. See complete history


Substrate-induced transmembrane signaling in the cobalamin transporter BtuB

Chimento, D.P.Mohanty, A.K.Kadner, R.J.Wiener, M.C.

(2003) Nat Struct Biol 10: 394-401

  • DOI: https://doi.org/10.1038/nsb914
  • Primary Citation of Related Structures:  
    1NQE, 1NQF, 1NQG, 1NQH

  • PubMed Abstract: 

    The outer membranes of Gram-negative bacteria possess transport proteins essential for uptake of scarce nutrients. In TonB-dependent transporters, a conserved sequence of seven residues, the Ton box, faces the periplasm and interacts with the inner membrane TonB protein to energize an active transport cycle. A critical mechanistic step is the structural change in the Ton box of the transporter upon substrate binding; this essential transmembrane signaling event increases the affinity of the transporter for TonB and enables active transport to proceed. We have solved crystal structures of BtuB, the outer membrane cobalamin transporter from Escherichia coli, in the absence and presence of cyanocobalamin (vitamin B(12)). In these structures, the Ton box is ordered and undergoes a conformational change in the presence of bound substrate. Calcium has been implicated as a necessary factor for the high-affinity binding (K(d) approximately 0.3 nM) of cyanocobalamin to BtuB. We observe two bound calcium ions that order three extracellular loops of BtuB, thus providing a direct (and unusual) structural role for calcium.

  • Organizational Affiliation

    Department of Microbiology, University of Virginia, Charlottesville, Virginia 22908, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vitamin B12 receptor594Escherichia coliMutation(s): 0 
Gene Names: btuB
Membrane Entity: Yes 
Find proteins for P06129 (Escherichia coli (strain K12))
Explore P06129 
Go to UniProtKB:  P06129
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06129
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.59α = 90
b = 81.59β = 90
c = 210.078γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata 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: 2003-04-29
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description