8XD7 | pdb_00008xd7

Cryo-EM structure of inhibitor 25a bound human urea transporter A2.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8XD7

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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 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.

Macromolecule Content 

  • Total Structure Weight: 131.98 kDa 
  • Atom Count: 7,599 
  • Modeled Residue Count: 984 
  • Deposited Residue Count: 1,191 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Urea transporter 2
A, B, C
397Homo sapiensMutation(s): 0 
Gene Names: SLC14A2HUT2UT2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15849 (Homo sapiens)
Explore Q15849 
Go to UniProtKB:  Q15849
PHAROS:  Q15849
GTEx:  ENSG00000132874 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15849
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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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