7K4B

Cryo-EM structure of human TRPV6 in complex with (4- phenylcyclohexyl)piperazine inhibitor cis-22a


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Inactivation-mimicking block of the epithelial calcium channel TRPV6.

Bhardwaj, R.Lindinger, S.Neuberger, A.Nadezhdin, K.D.Singh, A.K.Cunha, M.R.Derler, I.Gyimesi, G.Reymond, J.L.Hediger, M.A.Romanin, C.Sobolevsky, A.I.

(2020) Sci Adv 6

  • DOI: https://doi.org/10.1126/sciadv.abe1508
  • Primary Citation of Related Structures:  
    7D2K, 7K4A, 7K4B, 7K4C, 7K4D, 7K4E, 7K4F

  • PubMed Abstract: 

    Epithelial calcium channel TRPV6 plays vital roles in calcium homeostasis, and its dysregulation is implicated in multifactorial diseases, including cancers. Here, we study the molecular mechanism of selective nanomolar-affinity TRPV6 inhibition by (4-phenylcyclohexyl)piperazine derivatives (PCHPDs). We use x-ray crystallography and cryo-electron microscopy to solve the inhibitor-bound structures of TRPV6 and identify two types of inhibitor binding sites in the transmembrane region: (i) modulatory sites between the S1-S4 and pore domains normally occupied by lipids and (ii) the main site in the ion channel pore. Our structural data combined with mutagenesis, functional and computational approaches suggest that PCHPDs plug the open pore of TRPV6 and convert the channel into a nonconducting state, mimicking the action of calmodulin, which causes inactivation of TRPV6 channels under physiological conditions. This mechanism of inhibition explains the high selectivity and potency of PCHPDs and opens up unexplored avenues for the design of future-generation biomimetic drugs.


  • Organizational Affiliation

    Department of Nephrology and Hypertension and Department of Biomedical Research, University of Bern, Inselspital, Freiburgstrasse 15, CH-3010 Bern, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transient receptor potential cation channel subfamily V member 6
A, B, C, D
670Homo sapiensMutation(s): 0 
Gene Names: TRPV6ECAC2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H1D0 (Homo sapiens)
Explore Q9H1D0 
Go to UniProtKB:  Q9H1D0
PHAROS:  Q9H1D0
GTEx:  ENSG00000165125 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H1D0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PCW
Query on PCW

Download Ideal Coordinates CCD File 
AB [auth D]
BA [auth B]
BB [auth D]
CA [auth B]
CB [auth D]
AB [auth D],
BA [auth B],
BB [auth D],
CA [auth B],
CB [auth D],
DA [auth B],
EA [auth B],
EB [auth D],
FA [auth B],
FB [auth D],
G [auth A],
GA [auth B],
H [auth A],
HA [auth B],
HB [auth D],
I [auth A],
IA [auth B],
IB [auth D],
J [auth A],
JA [auth B],
JB [auth D],
K [auth A],
KA [auth B],
KB [auth D],
L [auth A],
LB [auth D],
M [auth A],
MA [auth C],
MB [auth D],
N [auth A],
NA [auth C],
NB [auth D],
O [auth A],
P [auth A],
QA [auth C],
RA [auth C],
S [auth A],
SA [auth C],
T [auth A],
TA [auth C],
UA [auth C],
VA [auth C],
W [auth B],
WA [auth C],
X [auth B],
XA [auth C],
YA [auth C],
ZA [auth C]
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H85 N O8 P
SNKAWJBJQDLSFF-NVKMUCNASA-O
Y01
Query on Y01

Download Ideal Coordinates CCD File 
AA [auth B]
DB [auth D]
F [auth A]
GB [auth D]
PA [auth C]
AA [auth B],
DB [auth D],
F [auth A],
GB [auth D],
PA [auth C],
R [auth A],
V [auth B],
Z [auth B]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
VUG (Subject of Investigation/LOI)
Query on VUG

Download Ideal Coordinates CCD File 
E [auth A],
LA [auth B],
OA [auth C],
Q [auth A],
Y [auth B]
1-[cis-4-(3-methylphenyl)cyclohexyl]-4-(pyridin-3-yl)piperazine
C22 H29 N3
QANXJBIOBLNORO-TYKWCNGQSA-N
CA
Query on CA

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

Experimental Data

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

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01 CA206573
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01 NS083660
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01 NS107253
National Science Foundation (NSF, United States)United States1818086
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM103310
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30 GM124165

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-09
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references