9NQ9 | pdb_00009nq9

Magnesium ions-bound closed-state cryo-EM structure of human TRPV6 in cNW11 nanodiscs

  • Classification: MEMBRANE PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2025-03-12 Released: 2025-11-19 
  • Deposition Author(s): Neuberger, A., Sobolevsky, A.I.
  • Funding Organization(s): German Research Foundation (DFG), National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.97 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

The locking mechanism of human TRPV6 inhibition by intracellular magnesium.

Neuberger, A.Shalygin, A.Veretenenko, I.I.Trofimov, Y.A.Gudermann, T.Chubanov, V.Efremov, R.G.Sobolevsky, A.I.

(2025) Nat Commun 16: 9826-9826

  • DOI: https://doi.org/10.1038/s41467-025-65919-1
  • Primary Citation of Related Structures:  
    9NQ9

  • PubMed Abstract: 

    TRPV6 is a member of the vanilloid subfamily of transient receptor potential channels, which serves as the master regulator of Ca 2+ homeostasis. TRPV6 functions as a constitutively active Ca 2+ channel, and emerging evidence indicates that its overactivity underpins the progression of several human diseases, including cancer. Hence, there is a pressing need to identify TRPV6 inhibitors in conjunction with a deep mechanistic understanding of their effects on the channel activity. Here we combine cryo-electron microscopy, mutagenesis, electrophysiology and molecular dynamics modeling to decipher the molecular mechanism of TRPV6 inhibition by intracellular Mg 2+ . Mg 2+ appears to bind to four, one per subunit, sites around the intracellular entrance to the TRPV6 channel pore, contributed by the negatively charged residues, D489 in the transmembrane helix S5 and D580 in S6. When bound to the D489-D580 site, Mg 2+ prevents the α-to-π transition in the middle of S6 that accompanies channel opening, thus maintaining S6 entirely α-helical, locking the channel in the closed state and inhibiting TRPV6-mediated currents. Further exploration of this inhibitory mechanism may help to develop future strategies for the treatment of TRPV6-associated diseases.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 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 6
A, B, C, D
612Homo sapiensMutation(s): 0 
Gene Names: TRPV6ECAC2
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POV
Query on POV

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
G [auth A]
GA [auth D]
H [auth A]
AA [auth C],
BA [auth C],
G [auth A],
GA [auth D],
H [auth A],
HA [auth D],
I [auth A],
IA [auth D],
J [auth A],
JA [auth D],
L [auth A],
S [auth B],
T [auth B],
U [auth B],
Y [auth C],
Z [auth C]
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
Y01
Query on Y01

Download Ideal Coordinates CCD File 
DA [auth D]
E [auth A]
EA [auth D]
F [auth A]
FA [auth D]
DA [auth D],
E [auth A],
EA [auth D],
F [auth A],
FA [auth D],
M [auth A],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
W [auth C],
X [auth C]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
CA [auth C],
K [auth A],
KA [auth D],
N [auth A],
V [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.97 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany464295817
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 Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)United StatesR01 AR078814

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-19
    Type: Initial release