6E2F | pdb_00006e2f

Cryo-EM structure of human TRPV6 in complex with Calmodulin

• PDB DOI: https://doi.org/10.2210/pdb6E2F/pdb
• EM Map EMD-8961: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens, Escherichia coli K-12
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2018-07-11 Released: 2018-08-22 
• Deposition Author(s): Singh, A.K., McGoldrick, L.L., Sobolevsky, A.I.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Mechanism of calmodulin inactivation of the calcium-selective TRP channel TRPV6.

Singh, A.K., McGoldrick, L.L., Twomey, E.C., Sobolevsky, A.I.

(2018) Sci Adv 4: eaau6088-eaau6088

• PubMed: 30116787 
• DOI: https://doi.org/10.1126/sciadv.aau6088
• Primary Citation Related Structures: 
  6E2F, 6E2G


• PubMed Abstract: 
  

  Calcium (Ca ²⁺ ) plays a major role in numerous physiological processes. Ca ²⁺ homeostasis is tightly controlled by ion channels, the aberrant regulation of which results in various diseases including cancers. Calmodulin (CaM)-mediated Ca ²⁺ -induced inactivation is an ion channel regulatory mechanism that protects cells against the toxic effects of Ca ²⁺ overload. We used cryo-electron microscopy to capture the epithelial calcium channel TRPV6 (transient receptor potential vanilloid subfamily member 6) inactivated by CaM. The TRPV6-CaM complex exhibits 1:1 stoichiometry; one TRPV6 tetramer binds both CaM lobes, which adopt a distinct head-to-tail arrangement. The CaM carboxyl-terminal lobe plugs the channel through a unique cation-π interaction by inserting the side chain of lysine K115 into a tetra-tryptophan cage at the pore's intracellular entrance. We propose a mechanism of CaM-mediated Ca ²⁺ -induced inactivation that can be explored for therapeutic design.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street, New York, NY 10032, USA.
Integrated Program in Cellular, Molecular and Biomedical Studies, Columbia University, New York, NY 10032, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A4B1 Local Symmetry: Cyclic - C4  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - A4 

Local Symmetry: Cyclic - C4  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 350.3 kDa 
• Atom Count: 21,204 
• Modeled Residue Count: 2,640 
• Deposited Residue Count: 3,049 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transient receptor potential cation channel subfamily V member 6	A, B, C, D	725	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 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	F [auth A], G [auth A], H [auth E], I [auth E], J [auth E], K [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-08-22 
Deposition Author(s): Singh, A.K., McGoldrick, L.L., Sobolevsky, A.I.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	1R01CA206573-01A1

Revision History  

• Version 1.0: 2018-08-22
  Type: Initial release
  
• Version 1.1: 2018-10-24
  Changes: Data collection, Database references
• Version 1.2: 2019-12-18
  Changes: Author supporting evidence, Other
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2025-05-28
  Changes: Data collection, Structure summary