Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 130.13 kDa 
• Atom Count: 8470 
• Modelled Residue Count: 1037 
• Deposited Residue Count: 1152 
• Unique protein chains: 1

4EZC

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

• DOI: 10.2210/pdb4EZC/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Bos taurus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2012-05-02 Released: 2012-06-27 
• Deposition Author(s): Cao, Y., Levin, E.J., Zhou, M., New York Consortium on Membrane Protein Structure (NYCOMPS)

---

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 

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

• PubMed: 22733730 
• 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. 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urea transporter 1	A, B, C	384	Bos taurus	Mutation(s): 0  Gene Names: SLC14A1, UT-B Membrane Entity: Yes
UniProt
Find proteins for Q5QF96 (Bos taurus) Explore Q5QF96  Go to UniProtKB:  Q5QF96

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SPL (Subject of Investigation/LOI)	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
BOG (Subject of Investigation/LOI)	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
BGC (Subject of Investigation/LOI)	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

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 = 74.703	α = 90
b = 105.645	β = 99
c = 105.87	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2012-05-02 
• Released Date: 2012-06-27 
Deposition Author(s): Cao, Y., Levin, E.J., Zhou, M., New York Consortium on Membrane Protein Structure (NYCOMPS)

Revision History  

• 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