4EZC

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history. 

Literature

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.USA 109: 11194-11199

  • DOI: 10.1073/pnas.1207362109
  • Primary Citation of Related Structures:  

  • 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 ure ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Urea transporter 1
A, B, C
384Bos taurusMutation(s): 0 
Gene Names: SLC14A1 (UT-B)
Membrane protein
mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Channels: Urea Transporters		Protein: 
UT-B Urea Transporter
Find proteins for Q5QF96 (Bos taurus)
Go to Gene View: SLC14A1
Go to UniProtKB:  Q5QF96
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPL
Query on SPL
Download SDF File 
Download CCD File 
A, B, C
OCTANOIC ACID (2-HYDROXY-1-HYDROXYMETHYL-HEPTADEC-3-ENYL)-AMIDE
CERAMIDE
C26 H51 N O3
APDLCSPGWPLYEQ-WUBHUQEYSA-N
 Ligand Interaction
BGC
Query on BGC
Download SDF File 
Download CCD File 
A, B, C
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
BOG
Query on BOG
Download SDF File 
Download CCD File 
A, B, C
B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 74.703α = 90.00
b = 105.645β = 99.00
c = 105.870γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-06-27
    Type: Initial release
  • Version 1.1: 2012-07-04
    Type: Database references
  • Version 1.2: 2012-07-25
    Type: Other
  • Version 1.3: 2013-01-09
    Type: Database references
  • Version 1.4: 2017-11-15
    Type: Refinement description