Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 68.56 kDa 
• Atom Count: 4733 
• Modelled Residue Count: 549 
• Deposited Residue Count: 594 
• Unique protein chains: 1

1NQE

OUTER MEMBRANE COBALAMIN TRANSPORTER (BTUB) FROM E. COLI

• PDB DOI: 10.2210/pdb1NQE/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2003-01-21 Released: 2003-04-29 
• Deposition Author(s): Chimento, D.P., Mohanty, A.K., Kadner, R.J., Wiener, M.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.232 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 

Literature

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

• PubMed: 12652322 
• DOI: 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.

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Related Citations: 

• Crystallization and initial X-ray diffraction of BtuB, the integral membrane cobalamin transporter of Escherichia coli
  Chimento, D.P., Mohanty, A.K., Kadner, R.J., Wiener, M.C.
  (2003) Acta Crystallogr D Biol Crystallogr 59: 509

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitamin B12 receptor	A	594	Escherichia coli	Mutation(s): 0  Gene Names: btuB Membrane Entity: Yes
UniProt
Find proteins for P06129 (Escherichia coli (strain K12)) Explore P06129  Go to UniProtKB:  P06129

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C8E	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE C16 H34 O5 FEOZZFHAVXYAMB-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 81.59	α = 90
b = 81.59	β = 90
c = 210.078	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-01-21 
• Released Date: 2003-04-29 
Deposition Author(s): Chimento, D.P., Mohanty, A.K., Kadner, R.J., Wiener, M.C.

Revision History  

• 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