9CUH

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

PDB DOI: https://doi.org/10.2210/pdb9CUH/pdb
EM Map EMD-45933: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes

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: 3.03 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

Structure-function analyses of human oncochannel TRPV6 variants associated with a racial divergence in susceptibility to cancer

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

(2024) Structure

DOI: https://doi.org/10.1016/j.str.2024.10.018

Macromolecule Content

Total Structure Weight: 382.85 kDa
Atom Count: 20,877
Modelled Residue Count: 2,376
Deposited Residue Count: 3,060
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	765	Homo sapiens	Mutation(s): 3 Gene Names: TRPV6, ECAC2
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 G [auth A] SDF format, chain HA [auth C] SDF format, chain V [auth B] SDF format, chain VA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth D]	G [auth A], HA [auth C], V [auth B], VA [auth D]	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₅ N O₈ P SNKAWJBJQDLSFF-NVKMUCNASA-O		Interactions Focus chain G [auth A] Focus chain HA [auth C] Focus chain V [auth B] Focus chain VA [auth D] Interactions & Density Focus chain G [auth A] Focus chain HA [auth C] Focus chain V [auth B] Focus chain VA [auth D]
POV Query on POV Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth D] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain EA [auth C] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain IA [auth C] SDF format, chain J [auth A] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain M [auth A] SDF format, chain MA [auth C] SDF format, chain N [auth A] SDF format, chain NA [auth C] SDF format, chain OA [auth C] SDF format, chain P [auth A] SDF format, chain PA [auth D] SDF format, chain QA [auth D] SDF format, chain S [auth B] SDF format, chain SA [auth D] SDF format, chain W [auth B] SDF format, chain WA [auth D] SDF format, chain X [auth B] SDF format, chain XA [auth D] SDF format, chain Y [auth B] SDF format, chain YA [auth D] SDF format, chain Z [auth B] SDF format, chain ZA [auth D] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth D] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth D] mmCIF format, chain AA [auth B] mmCIF format, chain AB [auth D] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain EA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain OA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain QA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth D] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth D] mmCIF format, chain Y [auth B] mmCIF format, chain YA [auth D] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth D]	AA [auth B] AB [auth D] BA [auth B] CA [auth B] EA [auth C] AA [auth B], AB [auth D], BA [auth B], CA [auth B], EA [auth C], H [auth A], I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], N [auth A], NA [auth C], OA [auth C], P [auth A], PA [auth D], QA [auth D], S [auth B], SA [auth D], W [auth B], WA [auth D], X [auth B], XA [auth D], Y [auth B], YA [auth D], Z [auth B], ZA [auth D]	(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 AB [auth D] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain EA [auth C] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain S [auth B] Focus chain SA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain EA [auth C] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain S [auth B] Focus chain SA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D]
Y01 Query on Y01 Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain O [auth A] SDF format, chain R [auth B] SDF format, chain RA [auth D] SDF format, chain T [auth B] SDF format, chain TA [auth D] SDF format, chain U [auth B] SDF format, chain UA [auth D] MOL2 format, chain DA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth D] mmCIF format, chain DA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth D] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth D] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth D]	DA [auth C] E [auth A] F [auth A] FA [auth C] GA [auth C] DA [auth C], E [auth A], F [auth A], FA [auth C], GA [auth C], O [auth A], R [auth B], RA [auth D], T [auth B], TA [auth D], U [auth B], UA [auth D]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain DA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain O [auth A] Focus chain R [auth B] Focus chain RA [auth D] Focus chain T [auth B] Focus chain TA [auth D] Focus chain U [auth B] Focus chain UA [auth D] Interactions & Density Focus chain DA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain O [auth A] Focus chain R [auth B] Focus chain RA [auth D] Focus chain T [auth B] Focus chain TA [auth D] Focus chain U [auth B] Focus chain UA [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain Q [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain Q [auth A]	Q [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Interactions & Density Focus chain Q [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.03 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

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