8XDH

Cryo-EM structure of zebrafish urea transporter.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural insights into the mechanisms of urea permeation and distinct inhibition modes of urea transporters.

Huang, S.M.Huang, Z.Z.Liu, L.Xiong, M.Y.Zhang, C.Cai, B.Y.Wang, M.W.Cai, K.Jia, Y.L.Wang, J.L.Zhang, M.H.Xie, Y.H.Li, M.Zhang, H.Weng, C.H.Wen, X.Li, Z.Sun, Y.Yi, F.Yang, Z.Xiao, P.Yang, F.Yu, X.Tie, L.Yang, B.X.Sun, J.P.

(2024) Nat Commun 15: 10226-10226

  • DOI: https://doi.org/10.1038/s41467-024-54305-y
  • Primary Citation of Related Structures:  
    8XD7, 8XD9, 8XDA, 8XDB, 8XDC, 8XDD, 8XDE, 8XDF, 8XDG, 8XDH, 8XDI

  • PubMed Abstract: 

    Urea's transmembrane transport through urea transporters (UT) is a fundamental physiological behavior for life activities. Here, we present 11 cryo-EM structures of four UT members in resting states, urea transport states, or inactive states bound with synthetic competitive, uncompetitive or noncompetitive inhibitor. Our results indicate that the binding of urea via a conserved urea recognition motif (URM) and the urea transport via H-bond transfer along the Q Pb -T 5b -T 5a -Q Pa motif among different UT members. Moreover, distinct binding modes of the competitive inhibitors 25a and ATB3, the uncompetitive inhibitor CF11 and the noncompetitive inhibitor HQA2 provide different mechanisms for blocking urea transport and achieved selectivity through L-P pocket, UCBP region and SCG pocket, respectively. In summary, our study not only allows structural understanding of urea transport via UTs but also afforded a structural landscape of hUT-A2 inhibition by competitive, uncompetitive and noncompetitive inhibitors, which may facilitate developing selective human UT-A inhibitors as a new class of salt-sparing diuretics.


  • Organizational Affiliation

    Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Beijing Key Laboratory of Cardiovascular Receptors Research, Peking University, Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Urea transporter
A, B, C
426Danio rerioMutation(s): 0 
Gene Names: slc14a2
Membrane Entity: Yes 
UniProt
Find proteins for A0A8M9Q878 (Danio rerio)
Explore A0A8M9Q878 
Go to UniProtKB:  A0A8M9Q878
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8M9Q878
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
URE
Query on URE

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth C],
O [auth C],
P [auth C],
Q [auth C],
R [auth C]
UREA
C H4 N2 O
XSQUKJJJFZCRTK-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82304601

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-04
    Type: Initial release