6D7Q

Crystal Structure of Rat TRPV6*-Y466A in complex with 2-Aminoethoxydiphenyl borate (2-APB)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.275 
  • R-Value Observed: 0.276 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural bases of TRP channel TRPV6 allosteric modulation by 2-APB.

Singh, A.K.Saotome, K.McGoldrick, L.L.Sobolevsky, A.I.

(2018) Nat Commun 9: 2465-2465

  • DOI: https://doi.org/10.1038/s41467-018-04828-y
  • Primary Citation of Related Structures:  
    6D7O, 6D7P, 6D7Q, 6D7S, 6D7T, 6D7V, 6D7X

  • PubMed Abstract: 

    Transient receptor potential (TRP) channels are involved in various physiological processes, including sensory transduction. The TRP channel TRPV6 mediates calcium uptake in epithelia and its expression is dramatically increased in numerous types of cancer. TRPV6 inhibitors suppress tumor growth, but the molecular mechanism of inhibition remains unknown. Here, we present crystal and cryo-EM structures of human and rat TRPV6 bound to 2-aminoethoxydiphenyl borate (2-APB), a TRPV6 inhibitor and modulator of numerous TRP channels. 2-APB binds to TRPV6 in a pocket formed by the cytoplasmic half of the S1-S4 transmembrane helix bundle. Comparing human wild-type and high-affinity mutant Y467A structures, we show that 2-APB induces TRPV6 channel closure by modulating protein-lipid interactions. Mutagenesis and functional analyses suggest that the identified 2-APB binding site might be present in other members of vanilloid subfamily TRP channels. Our findings reveal a mechanism of ion channel allosteric modulation that can be exploited for therapeutic design.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street, New York, NY, 10032, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transient receptor potential cation channel subfamily V member 6672Rattus norvegicusMutation(s): 1 
Gene Names: Trpv6
Membrane Entity: Yes 
UniProt
Find proteins for Q9R186 (Rattus norvegicus)
Explore Q9R186 
Go to UniProtKB:  Q9R186
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9R186
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FZ4
Query on FZ4

Download Ideal Coordinates CCD File 
B [auth A]2-aminoethyl diphenylborinate
C14 H16 B N O
BLZVCIGGICSWIG-UHFFFAOYSA-N
DTB
Query on DTB

Download Ideal Coordinates CCD File 
C [auth A]6-(5-METHYL-2-OXO-IMIDAZOLIDIN-4-YL)-HEXANOIC ACID
C10 H18 N2 O3
AUTOLBMXDDTRRT-JGVFFNPUSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.275 
  • R-Value Observed: 0.276 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.187α = 90
b = 145.187β = 90
c = 115.897γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United States1R01CA206573-01A1

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-18
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description