Crystal Structure of the UT-B Urea Transporter from Bos Taurus

Experimental Data Snapshot

  • Resolution: 2.36 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 

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This is version 1.6 of the entry. See complete history


Structure and permeation mechanism of a mammalian urea transporter.

Levin, E.J.Cao, Y.Enkavi, G.Quick, M.Pan, Y.Tajkhorshid, E.Zhou, M.

(2012) Proc Natl Acad Sci U S A 109: 11194-11199

  • DOI: https://doi.org/10.1073/pnas.1207362109
  • Primary Citation of Related Structures:  
    4EZC, 4EZD

  • PubMed Abstract: 

    As an adaptation to infrequent access to water, terrestrial mammals produce urine that is hyperosmotic to plasma. To prevent osmotic diuresis by the large quantity of urea generated by protein catabolism, the kidney epithelia contain facilitative urea transporters (UTs) that allow rapid equilibration between the urinary space and the hyperosmotic interstitium. Here we report the first X-ray crystal structure of a mammalian UT, UT-B, at a resolution of 2.36 Å. UT-B is a homotrimer and each protomer contains a urea conduction pore with a narrow selectivity filter. Structural analyses and molecular dynamics simulations showed that the selectivity filter has two urea binding sites separated by an approximately 5.0 kcal/mol energy barrier. Functional studies showed that the rate of urea conduction in UT-B is increased by hypoosmotic stress, and that the site of osmoregulation coincides with the location of the energy barrier.

  • Organizational Affiliation

    Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY 10032, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Urea transporter 1
A, B, C
384Bos taurusMutation(s): 0 
Gene Names: SLC14A1UT-B
Membrane Entity: Yes 
Find proteins for Q5QF96 (Bos taurus)
Explore Q5QF96 
Go to UniProtKB:  Q5QF96
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5QF96
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SPL

Download Ideal Coordinates CCD File 
J [auth A],
P [auth B],
X [auth C]
C26 H51 N O3
Query on BOG

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
N [auth B]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
N [auth B],
O [auth B],
T [auth C],
U [auth C],
V [auth C],
W [auth C]
octyl beta-D-glucopyranoside
C14 H28 O6
Query on BGC

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
K [auth B]
L [auth B]
M [auth B]
D [auth A],
E [auth A],
K [auth B],
L [auth B],
M [auth B],
Q [auth C],
R [auth C],
S [auth C]
C6 H12 O6
Experimental Data & Validation

Experimental Data

  • Resolution: 2.36 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.703α = 90
b = 105.645β = 99
c = 105.87γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data 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: 2012-06-27
    Type: Initial release
  • Version 1.1: 2012-07-04
    Changes: Database references
  • Version 1.2: 2012-07-25
    Changes: Other
  • Version 1.3: 2013-01-09
    Changes: Database references
  • Version 1.4: 2017-11-15
    Changes: Refinement description
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.6: 2024-02-28
    Changes: Data collection, Database references, Structure summary