5WO9

Crystal Structure of Transient Receptor Potential (TRP) channel TRPV6* in the presence of Calcium

• PDB DOI: https://doi.org/10.2210/pdb5WO9/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Homo sapiens
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMmpstruc


• Deposited: 2017-08-01 Released: 2017-09-13 
• Deposition Author(s): Singh, A.K., Saotome, K., Sobolevsky, A.I.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.70 Å
• R-Value Free: 0.316 
• R-Value Work: 0.272 
• R-Value Observed: 0.274 

Literature

Swapping of transmembrane domains in the epithelial calcium channel TRPV6.

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

(2017) Sci Rep 7: 10669-10669

• PubMed: 28878326 
• DOI: https://doi.org/10.1038/s41598-017-10993-9
• Primary Citation of Related Structures:  
  5WO6, 5WO7, 5WO8, 5WO9, 5WOA


• PubMed Abstract: 
  

  Tetrameric ion channels have either swapped or non-swapped arrangements of the S1-S4 and pore domains. Here we show that mutations in the transmembrane domain of TRPV6 can result in conversion from a domain-swapped to non-swapped fold. These results reveal structural determinants of domain swapping and raise the possibility that a single ion channel subtype can fold into either arrangement in vivo, affecting its function in normal or disease states.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 77.47 kDa 
• Atom Count: 4,773 
• Modelled Residue Count: 595 
• Deposited Residue Count: 672 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transient receptor potential cation channel subfamily V member 6	A	672	Rattus norvegicus	Mutation(s): 3  Gene Names: Trpv6 Membrane Entity: Yes
UniProt
Find proteins for Q9R186 (Rattus norvegicus) Explore Q9R186  Go to UniProtKB:  Q9R186

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DTB	B [auth A]	6-(5-METHYL-2-OXO-IMIDAZOLIDIN-4-YL)-HEXANOIC ACID C10 H18 N2 O3 AUTOLBMXDDTRRT-JGVFFNPUSA-N
CA	C [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.70 Å
• R-Value Free: 0.316 
• R-Value Work: 0.272 
• R-Value Observed: 0.274 
• Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.48	α = 90
b = 145.48	β = 90
c = 110.95	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-09-13 
Deposition Author(s): Singh, A.K., Saotome, K., Sobolevsky, A.I.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01 CA206573

Revision History  

• Version 1.0: 2017-09-13
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence, Database references
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description