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 
  • R-Value Observed: 0.197 

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This is version 1.5 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 U S A 109: 11194-11199

  • DOI: 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 ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Urea transporter 1A, B, C384Bos taurusMutation(s): 0 
Gene Names: SLC14A1, UT-B
Membrane Entity: Yes 
UniProt
Find proteins for Q5QF96 (Bos taurus)
Explore Q5QF96 
Go to UniProtKB:  Q5QF96
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5QF96
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPL
Query on SPL
Download Ideal Coordinates CCD File 
J [auth A],
P [auth B],
X [auth C]		OCTANOIC ACID (2-HYDROXY-1-HYDROXYMETHYL-HEPTADEC-3-ENYL)-AMIDE
C26 H51 N O3
APDLCSPGWPLYEQ-WUBHUQEYSA-N		 Ligand Interaction
BOG
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
HEGSGKPQLMEBJL-RKQHYHRCSA-N		 Ligand Interaction
BGC
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]
beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-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 
  • 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
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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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