9CUJ | pdb_00009cuj

Structure of human full-length derived TRPV6 channel in apo open state

PDB DOI: https://doi.org/10.2210/pdb9CUJ/pdb
EM Map EMD-45935: EMDB EMDataResource

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

Deposited: 2024-07-26 Released: 2024-11-13
Deposition Author(s): Neuberger, A., Nadezhdin, K.D., Sobolevsky, A.I.
Funding Organization(s): National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS), National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), German Research Foundation (DFG)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.78 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structure-function analyses of human TRPV6 ancestral and derived haplotypes.

Neuberger, A., Shalygin, A., Trofimov, Y.A., Veretenenko, I.I., Nadezhdin, K.D., Krylov, N.A., Gudermann, T., Efremov, R.G., Chubanov, V., Sobolevsky, A.I.

(2025) Structure 33: 91-103.e5

PubMed: 39500315 Search on PubMed
DOI: https://doi.org/10.1016/j.str.2024.10.018
Primary Citation Related Structures:
9CUH, 9CUI, 9CUJ, 9CUK

PubMed Abstract:
TRPV6 is a Ca ²⁺ selective channel that mediates calcium uptake in the gut and contributes to the development and progression of human cancers. TRPV6 is represented by the ancestral and derived haplotypes that differ by three non-synonymous polymorphisms, located in the N-terminal ankyrin repeat domain (C157R), S1-S2 extracellular loop (M378V), and C-terminus (M681T). The ancestral and derived haplotypes were proposed to serve as genomic factors causing a different outcome for cancer patients of African ancestry. We solved cryoelectron microscopy (cryo-EM) structures of ancestral and derived TRPV6 in the open and calmodulin (CaM)-bound inactivated states. Neither state shows substantial structural differences caused by the non-synonymous polymorphisms. Functional properties assessed by electrophysiological recordings and Ca ²⁺ uptake measurements, and water and ion permeation evaluated by molecular modeling also appear similar between the haplotypes. Therefore, ancestral and derived TRPV6 have similar structure and function, implying that other factors are responsible for the differences in susceptibility to cancer.

Organizational Affiliation

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.

Macromolecule Content

Total Structure Weight: 395.48 kDa
Atom Count: 21,557
Modeled Residue Count: 2,440
Deposited Residue Count: 3,060
Unique protein chains: 1

Macromolecules

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| 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	765	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 BB [auth D] SDF format, chain XA [auth C] SDF format, chain WA [auth C] SDF format, chain VA [auth C] SDF format, chain UA [auth C] SDF format, chain R [auth A] SDF format, chain QB [auth D] SDF format, chain PB [auth D] SDF format, chain OB [auth D] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain KA [auth B] SDF format, chain HA [auth B] SDF format, chain GA [auth B] SDF format, chain FA [auth B] SDF format, chain EB [auth D] SDF format, chain EA [auth B] SDF format, chain AB [auth C] MOL2 format, chain BB [auth D] MOL2 format, chain XA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain UA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain QB [auth D] MOL2 format, chain PB [auth D] MOL2 format, chain OB [auth D] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain EB [auth D] MOL2 format, chain EA [auth B] MOL2 format, chain AB [auth C] mmCIF format, chain BB [auth D] mmCIF format, chain XA [auth C] mmCIF format, chain WA [auth C] mmCIF format, chain VA [auth C] mmCIF format, chain UA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain QB [auth D] mmCIF format, chain PB [auth D] mmCIF format, chain OB [auth D] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain EB [auth D] mmCIF format, chain EA [auth B] mmCIF format, chain AB [auth C]	AB [auth C] BB [auth D] EA [auth B] EB [auth D] FA [auth B] AB [auth C], BB [auth D], EA [auth B], EB [auth D], FA [auth B], GA [auth B], HA [auth B], KA [auth B], L [auth A], M [auth A], N [auth A], O [auth A], OB [auth D], PB [auth D], QB [auth D], R [auth A], UA [auth C], VA [auth C], WA [auth C], XA [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 BB [auth D] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain KA [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OB [auth D] Focus chain PB [auth D] Focus chain QB [auth D] Focus chain R [auth A] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Interactions & Density Focus chain AB [auth C] Focus chain BB [auth D] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain KA [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OB [auth D] Focus chain PB [auth D] Focus chain QB [auth D] Focus chain R [auth A] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C]
POV Query on POV Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain ZA [auth C] SDF format, chain Z [auth B] SDF format, chain YA [auth C] SDF format, chain W [auth B] SDF format, chain TA [auth C] SDF format, chain T [auth A] SDF format, chain SA [auth C] SDF format, chain RA [auth C] SDF format, chain QA [auth C] SDF format, chain Q [auth A] SDF format, chain PA [auth C] SDF format, chain P [auth A] SDF format, chain NB [auth D] SDF format, chain MB [auth D] SDF format, chain MA [auth C] SDF format, chain LB [auth D] SDF format, chain KB [auth D] SDF format, chain K [auth A] SDF format, chain JB [auth D] SDF format, chain JA [auth B] SDF format, chain IA [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain GB [auth D] SDF format, chain G [auth A] SDF format, chain DB [auth D] SDF format, chain DA [auth B] SDF format, chain CB [auth D] SDF format, chain CA [auth B] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain ZA [auth C] MOL2 format, chain Z [auth B] MOL2 format, chain YA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain TA [auth C] MOL2 format, chain T [auth A] MOL2 format, chain SA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain NB [auth D] MOL2 format, chain MB [auth D] MOL2 format, chain MA [auth C] MOL2 format, chain LB [auth D] MOL2 format, chain KB [auth D] MOL2 format, chain K [auth A] MOL2 format, chain JB [auth D] MOL2 format, chain JA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain GB [auth D] MOL2 format, chain G [auth A] MOL2 format, chain DB [auth D] MOL2 format, chain DA [auth B] MOL2 format, chain CB [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain ZA [auth C] mmCIF format, chain Z [auth B] mmCIF format, chain YA [auth C] mmCIF format, chain W [auth B] mmCIF format, chain TA [auth C] mmCIF format, chain T [auth A] mmCIF format, chain SA [auth C] mmCIF format, chain RA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain PA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain NB [auth D] mmCIF format, chain MB [auth D] mmCIF format, chain MA [auth C] mmCIF format, chain LB [auth D] mmCIF format, chain KB [auth D] mmCIF format, chain K [auth A] mmCIF format, chain JB [auth D] mmCIF format, chain JA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain GB [auth D] mmCIF format, chain G [auth A] mmCIF format, chain DB [auth D] mmCIF format, chain DA [auth B] mmCIF format, chain CB [auth D] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] CA [auth B] CB [auth D] DA [auth B] AA [auth B], BA [auth B], CA [auth B], CB [auth D], DA [auth B], DB [auth D], G [auth A], GB [auth D], H [auth A], I [auth A], IA [auth B], J [auth A], JA [auth B], JB [auth D], K [auth A], KB [auth D], LB [auth D], MA [auth C], MB [auth D], NB [auth D], P [auth A], PA [auth C], Q [auth A], QA [auth C], RA [auth C], SA [auth C], T [auth A], TA [auth C], W [auth B], YA [auth C], Z [auth B], ZA [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 CA [auth B] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain G [auth A] Focus chain GB [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JB [auth D] Focus chain K [auth A] Focus chain KB [auth D] Focus chain LB [auth D] Focus chain MA [auth C] Focus chain MB [auth D] Focus chain NB [auth D] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [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 W [auth B] Focus chain YA [auth C] Focus chain Z [auth B] Focus chain ZA [auth C] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain G [auth A] Focus chain GB [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JB [auth D] Focus chain K [auth A] Focus chain KB [auth D] Focus chain LB [auth D] Focus chain MA [auth C] Focus chain MB [auth D] Focus chain NB [auth D] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [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 W [auth B] Focus chain YA [auth C] Focus chain Z [auth B] Focus chain ZA [auth C]
Y01 Query on Y01 Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain V [auth B] SDF format, chain S [auth A] SDF format, chain OA [auth C] SDF format, chain NA [auth C] SDF format, chain LA [auth C] SDF format, chain IB [auth D] SDF format, chain HB [auth D] SDF format, chain FB [auth D] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain V [auth B] MOL2 format, chain S [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain IB [auth D] MOL2 format, chain HB [auth D] MOL2 format, chain FB [auth D] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain V [auth B] mmCIF format, chain S [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain NA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain IB [auth D] mmCIF format, chain HB [auth D] mmCIF format, chain FB [auth D] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	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] mmCIF 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: 2.78 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.18

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-11-13

Deposition Author(s):

Neuberger, A.

Nadezhdin, K.D.

Sobolevsky, A.I.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)	United States	R01 AR078814
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01 CA206573
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R01 NS083660
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R01 NS107253
German Research Foundation (DFG)	Germany	464295817