9CUI

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

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 1.0 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: 405.92 kDa
Atom Count: 22,713
Modelled Residue Count: 2,650
Deposited Residue Count: 3,209
Unique protein chains: 2

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

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 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 GB [auth D] SDF format, chain HA [auth B] SDF format, chain HB [auth D] SDF format, chain IA [auth B] SDF format, chain IB [auth D] SDF format, chain J [auth A] SDF format, chain JB [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain KB [auth D] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain QA [auth C] SDF format, chain R [auth A] SDF format, chain RA [auth C] SDF format, chain SA [auth C] 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 BA [auth B] SDF format, chain GA [auth B] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain PA [auth C] SDF format, chain T [auth A] SDF format, chain WA [auth C] SDF format, chain ZA [auth D] MOL2 format, chain AB [auth D] 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 GB [auth D] MOL2 format, chain HA [auth B] MOL2 format, chain HB [auth D] MOL2 format, chain IA [auth B] MOL2 format, chain IB [auth D] MOL2 format, chain J [auth A] MOL2 format, chain JB [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain KB [auth D] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain SA [auth C] 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 BA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain T [auth A] MOL2 format, chain WA [auth C] MOL2 format, chain ZA [auth D] mmCIF format, chain AB [auth D] 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 GB [auth D] mmCIF format, chain HA [auth B] mmCIF format, chain HB [auth D] mmCIF format, chain IA [auth B] mmCIF format, chain IB [auth D] mmCIF format, chain J [auth A] mmCIF format, chain JB [auth D] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain KB [auth D] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth C] mmCIF format, chain SA [auth C] 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 BA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain PA [auth C] mmCIF format, chain T [auth A] mmCIF format, chain WA [auth C] mmCIF format, chain ZA [auth D]	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 F [auth A] SDF format, chain MA [auth C] SDF format, chain OA [auth C] SDF format, chain S [auth A] SDF format, chain W [auth B] SDF format, chain Y [auth B] SDF format, chain AA [auth B] SDF 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 W [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain AA [auth B] MOL2 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 W [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain CB [auth D]	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 MB [auth E] SDF format, chain NB [auth E] SDF format, chain OB [auth E] SDF format, chain U [auth A] SDF format, chain V [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain LB [auth E] MOL2 format, chain MB [auth E] MOL2 format, chain NB [auth E] MOL2 format, chain OB [auth E] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain LB [auth E] mmCIF format, chain MB [auth E] mmCIF format, chain NB [auth E] mmCIF format, chain OB [auth E] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A]	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

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