7S88

Open apo-state cryo-EM structure of human TRPV6 in glyco-diosgenin detergent

PDB DOI: https://doi.org/10.2210/pdb7S88/pdb
EM Map EMD-24890: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMDmpstruc

Deposited: 2021-09-17 Released: 2021-11-17
Deposition Author(s): Neuberger, A., Nadezhdin, K.D., Sobolevsky, A.I.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), National Science Foundation (NSF, United States), German Research Foundation (DFG)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.69 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural mechanisms of TRPV6 inhibition by ruthenium red and econazole.

Neuberger, A., Nadezhdin, K.D., Sobolevsky, A.I.

(2021) Nat Commun 12: 6284-6284

PubMed: 34725357 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41467-021-26608-x
Primary Citation of Related Structures:
7S88, 7S89, 7S8B, 7S8C

PubMed Abstract:
TRPV6 is a calcium-selective ion channel implicated in epithelial Ca ²⁺ uptake. TRPV6 inhibitors are needed for the treatment of a broad range of diseases associated with disturbed calcium homeostasis, including cancers. Here we combine cryo-EM, calcium imaging, and mutagenesis to explore molecular bases of human TRPV6 inhibition by the antifungal drug econazole and the universal ion channel blocker ruthenium red (RR). Econazole binds to an allosteric site at the channel's periphery, where it replaces a lipid. In contrast, RR inhibits TRPV6 by binding in the middle of the ion channel's selectivity filter and plugging its pore like a bottle cork. Despite different binding site locations, both inhibitors induce similar conformational changes in the channel resulting in closure of the gate formed by S6 helices bundle crossing. The uncovered molecular mechanisms of TRPV6 inhibition can guide the design of a new generation of clinically useful inhibitors.

Organizational Affiliation

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.

Macromolecule Content

Total Structure Weight: 359.63 kDa
Atom Count: 22,201
Modelled Residue Count: 2,456
Deposited Residue Count: 2,732
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transient receptor potential cation channel subfamily V member 6	A, B, C, D	683	Homo sapiens	Mutation(s): 0 Gene Names: TRPV6, ECAC2 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9H1D0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PCW Query on PCW Download Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain DB [auth D] SDF format, chain G [auth A] SDF format, chain GA [auth B] SDF format, chain JA [auth B] SDF format, chain JB [auth D] SDF format, chain KA [auth B] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain PA [auth C] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain WA [auth C] SDF format, chain ZA [auth C] SDF format, chain EB [auth D] SDF format, chain FA [auth B] SDF format, chain PB [auth D] SDF format, chain QB [auth D] SDF format, chain VA [auth C] SDF format, chain Z [auth B] MOL2 format, chain AB [auth C] MOL2 format, chain DB [auth D] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain JB [auth D] MOL2 format, chain KA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain WA [auth C] MOL2 format, chain ZA [auth C] MOL2 format, chain EB [auth D] MOL2 format, chain FA [auth B] MOL2 format, chain PB [auth D] MOL2 format, chain QB [auth D] MOL2 format, chain VA [auth C] MOL2 format, chain Z [auth B]	AB [auth C] DB [auth D] EB [auth D] FA [auth B] G [auth A] AB [auth C], DB [auth D], EB [auth D], FA [auth B], G [auth A], GA [auth B], JA [auth B], JB [auth D], KA [auth B], M [auth A], N [auth A], PA [auth C], PB [auth D], Q [auth A], QB [auth D], R [auth A], VA [auth C], WA [auth C], Z [auth B], ZA [auth C]	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₅ N O₈ P SNKAWJBJQDLSFF-NVKMUCNASA-O		Interactions Focus chain AB [auth C] Focus chain DB [auth D] Focus chain EB [auth D] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain JA [auth B] Focus chain JB [auth D] Focus chain KA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain PA [auth C] Focus chain PB [auth D] Focus chain Q [auth A] Focus chain QB [auth D] Focus chain R [auth A] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain Z [auth B] Focus chain ZA [auth C] Interactions & Density Focus chain AB [auth C] Focus chain DB [auth D] Focus chain EB [auth D] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain JA [auth B] Focus chain JB [auth D] Focus chain KA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain PA [auth C] Focus chain PB [auth D] Focus chain Q [auth A] Focus chain QB [auth D] Focus chain R [auth A] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain Z [auth B] Focus chain ZA [auth C]
POV Query on POV Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BB [auth D] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain GB [auth D] SDF format, chain HA [auth B] SDF format, chain L [auth A] SDF format, chain LB [auth D] SDF format, chain MB [auth D] SDF format, chain NB [auth D] SDF format, chain OB [auth D] SDF format, chain P [auth A] SDF format, chain QA [auth C] SDF format, chain RA [auth C] SDF format, chain T [auth A] SDF format, chain UA [auth C] SDF format, chain W [auth B] SDF format, chain YA [auth C] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain CB [auth D] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain IA [auth B] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain KB [auth D] SDF format, chain MA [auth C] SDF format, chain O [auth A] SDF format, chain SA [auth C] SDF format, chain TA [auth C] SDF format, chain XA [auth C] MOL2 format, chain AA [auth B] MOL2 format, chain BB [auth D] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain GB [auth D] MOL2 format, chain HA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain LB [auth D] MOL2 format, chain MB [auth D] MOL2 format, chain NB [auth D] MOL2 format, chain OB [auth D] MOL2 format, chain P [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain T [auth A] MOL2 format, chain UA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain YA [auth C] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain CB [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain KB [auth D] MOL2 format, chain MA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain SA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain XA [auth C]	AA [auth B] BA [auth B] BB [auth D] CA [auth B] CB [auth D] AA [auth B], BA [auth B], BB [auth D], CA [auth B], CB [auth D], DA [auth B], EA [auth B], GB [auth D], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], K [auth A], KB [auth D], L [auth A], LB [auth D], MA [auth C], MB [auth D], NB [auth D], O [auth A], OB [auth D], P [auth A], QA [auth C], RA [auth C], SA [auth C], T [auth A], TA [auth C], UA [auth C], W [auth B], XA [auth C], YA [auth C]	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-PFDVCBLKSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain GB [auth D] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain KB [auth D] Focus chain L [auth A] Focus chain LB [auth D] Focus chain MA [auth C] Focus chain MB [auth D] Focus chain NB [auth D] Focus chain O [auth A] Focus chain OB [auth D] Focus chain P [auth A] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain T [auth A] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain W [auth B] Focus chain XA [auth C] Focus chain YA [auth C] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain GB [auth D] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain KB [auth D] Focus chain L [auth A] Focus chain LB [auth D] Focus chain MA [auth C] Focus chain MB [auth D] Focus chain NB [auth D] Focus chain O [auth A] Focus chain OB [auth D] Focus chain P [auth A] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain T [auth A] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain W [auth B] Focus chain XA [auth C] Focus chain YA [auth C]
Y01 Query on Y01 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain FB [auth D] SDF format, chain HB [auth D] SDF format, chain OA [auth C] SDF format, chain S [auth A] SDF format, chain X [auth B] SDF format, chain IB [auth D] SDF format, chain LA [auth C] SDF format, chain NA [auth C] SDF format, chain V [auth B] SDF format, chain Y [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain FB [auth D] MOL2 format, chain HB [auth D] MOL2 format, chain OA [auth C] MOL2 format, chain S [auth A] MOL2 format, chain X [auth B] MOL2 format, chain IB [auth D] MOL2 format, chain LA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain V [auth B] MOL2 format, chain Y [auth B]	E [auth A] F [auth A] FB [auth D] HB [auth D] IB [auth D] E [auth A], F [auth A], FB [auth D], HB [auth D], IB [auth D], LA [auth C], NA [auth C], OA [auth C], S [auth A], V [auth B], X [auth B], Y [auth B]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain FB [auth D] Focus chain HB [auth D] Focus chain IB [auth D] Focus chain LA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain S [auth A] Focus chain V [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain FB [auth D] Focus chain HB [auth D] Focus chain IB [auth D] Focus chain LA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain S [auth A] Focus chain V [auth B] Focus chain X [auth B] Focus chain Y [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain U [auth A] MOL2 format, chain U [auth A]	U [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain U [auth A] Interactions & Density Focus chain U [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.69 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	3.1

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-11-17

Deposition Author(s):

Neuberger, A.

Nadezhdin, K.D.

Sobolevsky, A.I.

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	Germany	R01 CA206573
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	Germany	R01 NS083660
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	Germany	R01 NS107253
National Science Foundation (NSF, United States)	Germany	1818086
German Research Foundation (DFG)	Germany	464295817