9CUI

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

  • Classification: MEMBRANE PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): Yes 
  • Membrane Protein: Yes  PDBTM

  • 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 1.1 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.

(2024) Structure 

  • DOI: https://doi.org/10.1016/j.str.2024.10.018
  • Primary Citation of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transient receptor potential cation channel subfamily V member 6
A, B, C, D
765Homo sapiensMutation(s): 3 
Gene Names: TRPV6ECAC2
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H1D0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Calmodulin-1149Homo sapiensMutation(s): 0 
Gene Names: CALM1CALMCAMCAM1
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DP23
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PCW
Query on PCW

Download Ideal Coordinates CCD File 
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
Y01
Query on Y01

Download Ideal Coordinates CCD File 
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
CLR
Query on CLR

Download Ideal Coordinates CCD File 
DB [auth D],
G [auth A],
NA [auth C],
Z [auth B]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
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
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


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)United StatesR01 AR078814
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01 CA206573
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01 NS083660
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01 NS107253
German Research Foundation (DFG)Germany464295817

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-13
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Data collection, Database references