9CUI | pdb_00009cui

Structure of human full-length ancestral TRPV6 channel in Calmodulin-bound state

PDB DOI: https://doi.org/10.2210/pdb9CUI/pdb
EM Map EMD-45934: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes
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: 3.42 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.3 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: 405.92 kDa
Atom Count: 22,713
Modeled Residue Count: 2,650
Deposited Residue Count: 3,209
Unique protein chains: 2

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): 3 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

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Calmodulin-1	E	149	Homo sapiens	Mutation(s): 0 Gene Names: CALM1, CALM, CAM, CAM1
UniProt & NIH Common Fund Data Resources
Find proteins for P0DP23 (Homo sapiens) Explore P0DP23 Go to UniProtKB: P0DP23
PHAROS: P0DP23 GTEx: ENSG00000198668
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DP23
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 D] SDF format, chain BA [auth B] SDF format, chain BB [auth D] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain EB [auth D] SDF format, chain FA [auth B] SDF format, chain FB [auth D] SDF format, chain GA [auth B] SDF format, chain GB [auth D] SDF format, chain HA [auth B] SDF format, chain HB [auth D] SDF format, chain I [auth A] SDF format, chain IA [auth B] SDF format, chain JB [auth D] SDF format, chain KB [auth D] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain N [auth A] SDF format, chain PA [auth C] SDF format, chain QA [auth C] SDF format, chain R [auth A] SDF format, chain RA [auth C] SDF format, chain T [auth A] SDF format, chain TA [auth C] SDF format, chain UA [auth C] SDF format, chain VA [auth C] SDF format, chain X [auth B] SDF format, chain XA [auth D] SDF format, chain YA [auth D] SDF format, chain ZA [auth D] SDF format, chain WA [auth C] SDF format, chain SA [auth C] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain M [auth A] SDF format, chain KA [auth C] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain IB [auth D] SDF format, chain H [auth A] MOL2 format, chain AB [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth D] MOL2 format, chain FA [auth B] MOL2 format, chain FB [auth D] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth D] MOL2 format, chain HA [auth B] MOL2 format, chain HB [auth D] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain JB [auth D] MOL2 format, chain KB [auth D] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth C] MOL2 format, chain UA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth D] MOL2 format, chain YA [auth D] MOL2 format, chain ZA [auth D] MOL2 format, chain WA [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain M [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain IB [auth D] MOL2 format, chain H [auth A] mmCIF format, chain AB [auth D] mmCIF format, chain BA [auth B] mmCIF format, chain BB [auth D] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain EB [auth D] mmCIF format, chain FA [auth B] mmCIF format, chain FB [auth D] mmCIF format, chain GA [auth B] mmCIF format, chain GB [auth D] mmCIF format, chain HA [auth B] mmCIF format, chain HB [auth D] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain JB [auth D] mmCIF format, chain KB [auth D] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain PA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth C] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth C] mmCIF format, chain UA [auth C] mmCIF format, chain VA [auth C] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth D] mmCIF format, chain YA [auth D] mmCIF format, chain ZA [auth D] mmCIF format, chain WA [auth C] mmCIF format, chain SA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain M [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain IB [auth D] mmCIF format, chain H [auth A]	AB [auth D] BA [auth B] BB [auth D] CA [auth B] DA [auth B] AB [auth D], BA [auth B], BB [auth D], CA [auth B], DA [auth B], EA [auth B], EB [auth D], FA [auth B], FB [auth D], GA [auth B], GB [auth D], H [auth A], HA [auth B], HB [auth D], I [auth A], IA [auth B], IB [auth D], J [auth A], JB [auth D], K [auth A], KA [auth C], KB [auth D], L [auth A], LA [auth C], M [auth A], N [auth A], O [auth A], P [auth A], PA [auth C], Q [auth A], QA [auth C], R [auth A], RA [auth C], SA [auth C], T [auth A], TA [auth C], UA [auth C], VA [auth C], WA [auth C], X [auth B], XA [auth D], YA [auth D], ZA [auth D]	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₅ N O₈ P SNKAWJBJQDLSFF-NVKMUCNASA-O		Interactions Focus chain AB [auth D] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain H [auth A] Focus chain HA [auth B] Focus chain HB [auth D] Focus chain I [auth A] Focus chain IA [auth B] Focus chain IB [auth D] Focus chain J [auth A] Focus chain JB [auth D] Focus chain K [auth A] Focus chain KA [auth C] Focus chain KB [auth D] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] 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 VA [auth C] Focus chain WA [auth C] Focus chain X [auth B] Focus chain XA [auth D] Focus chain YA [auth D] Focus chain ZA [auth D] Interactions & Density Focus chain AB [auth D] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain H [auth A] Focus chain HA [auth B] Focus chain HB [auth D] Focus chain I [auth A] Focus chain IA [auth B] Focus chain IB [auth D] Focus chain J [auth A] Focus chain JB [auth D] Focus chain K [auth A] Focus chain KA [auth C] Focus chain KB [auth D] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] 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 VA [auth C] Focus chain WA [auth C] Focus chain X [auth B] Focus chain XA [auth D] Focus chain YA [auth D] Focus chain ZA [auth D]
Y01 Query on Y01 Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain CB [auth D] SDF format, chain F [auth A] SDF format, chain MA [auth C] SDF format, chain OA [auth C] SDF format, chain S [auth A] SDF format, chain Y [auth B] SDF format, chain W [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain CB [auth D] MOL2 format, chain F [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain S [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain W [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain CB [auth D] mmCIF format, chain F [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain OA [auth C] mmCIF format, chain S [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain W [auth B]	AA [auth B] CB [auth D] F [auth A] MA [auth C] OA [auth C] AA [auth B], CB [auth D], F [auth A], MA [auth C], OA [auth C], S [auth A], W [auth B], Y [auth B]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain AA [auth B] Focus chain CB [auth D] Focus chain F [auth A] Focus chain MA [auth C] Focus chain OA [auth C] Focus chain S [auth A] Focus chain W [auth B] Focus chain Y [auth B] Interactions & Density Focus chain AA [auth B] Focus chain CB [auth D] Focus chain F [auth A] Focus chain MA [auth C] Focus chain OA [auth C] Focus chain S [auth A] Focus chain W [auth B] Focus chain Y [auth B]
CLR Query on CLR Download:Ideal Coordinates CCD File SDF format, chain DB [auth D] SDF format, chain G [auth A] SDF format, chain NA [auth C] SDF format, chain Z [auth B] MOL2 format, chain DB [auth D] MOL2 format, chain G [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain Z [auth B] mmCIF format, chain DB [auth D] mmCIF format, chain G [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain Z [auth B]	DB [auth D], G [auth A], NA [auth C], Z [auth B]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain DB [auth D] Focus chain G [auth A] Focus chain NA [auth C] Focus chain Z [auth B] Interactions & Density Focus chain DB [auth D] Focus chain G [auth A] Focus chain NA [auth C] Focus chain Z [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain JA [auth B] SDF format, chain LB [auth E] SDF format, chain NB [auth E] SDF format, chain V [auth A] SDF format, chain U [auth A] SDF format, chain OB [auth E] SDF format, chain MB [auth E] MOL2 format, chain JA [auth B] MOL2 format, chain LB [auth E] MOL2 format, chain NB [auth E] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain OB [auth E] MOL2 format, chain MB [auth E] mmCIF format, chain JA [auth B] mmCIF format, chain LB [auth E] mmCIF format, chain NB [auth E] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain OB [auth E] mmCIF format, chain MB [auth E]	JA [auth B] LB [auth E] MB [auth E] NB [auth E] OB [auth E] JA [auth B], LB [auth E], MB [auth E], NB [auth E], OB [auth E], U [auth A], V [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain JA [auth B] Focus chain LB [auth E] Focus chain MB [auth E] Focus chain NB [auth E] Focus chain OB [auth E] Focus chain U [auth A] Focus chain V [auth A] Interactions & Density Focus chain JA [auth B] Focus chain LB [auth E] Focus chain MB [auth E] Focus chain NB [auth E] Focus chain OB [auth E] Focus chain U [auth A] Focus chain V [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.42 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

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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