6O20

Cryo-EM structure of TRPV5 with calmodulin bound

• PDB DOI: https://doi.org/10.2210/pdb6O20/pdb
• EM Map EMD-0607: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Oryctolagus cuniculus, Bos taurus
• Expression System: Homo sapiens, Escherichia coli-Pichia pastoris shuttle vector pPpARG4
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2019-02-22 Released: 2019-04-24 
• Deposition Author(s): Dang, S., van Goor, M.K., Asarnow, D., Wang, Y., Julius, D., Cheng, Y., van der Wijst, J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Center for Research Resources (NIH/NCRR), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), Netherlands Organisation for Scientific Research (NWO), European Union (EU), Human Frontier Science Program (HFSP), Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural insight into TRPV5 channel function and modulation.

Dang, S., van Goor, M.K., Asarnow, D., Wang, Y., Julius, D., Cheng, Y., van der Wijst, J.

(2019) Proc Natl Acad Sci U S A 116: 8869-8878

• PubMed: 30975749 
• DOI: https://doi.org/10.1073/pnas.1820323116
• Primary Citation of Related Structures:  
  6O1N, 6O1P, 6O1U, 6O20


• PubMed Abstract: 
  

  TRPV5 (transient receptor potential vanilloid 5) is a unique calcium-selective TRP channel essential for calcium homeostasis. Unlike other TRPV channels, TRPV5 and its close homolog, TRPV6, do not exhibit thermosensitivity or ligand-dependent activation but are constitutively open at physiological membrane potentials and modulated by calmodulin (CaM) in a calcium-dependent manner. Here we report high-resolution electron cryomicroscopy structures of truncated and full-length TRPV5 in lipid nanodiscs, as well as of a TRPV5 W583A mutant and TRPV5 in complex with CaM. These structures highlight the mechanism of calcium regulation and reveal a flexible stoichiometry of CaM binding to TRPV5.

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Organizational Affiliation: 

Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A4B1C1 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: gel filtration

Macromolecule Content

• Total Structure Weight: 433.68 kDa 
• Atom Count: 20,950 
• Modelled Residue Count: 2,624 
• Deposited Residue Count: 3,819 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transient receptor potential cation channel subfamily V member 5	A, B [auth E], D [auth B], E [auth C], F [auth D]	730	Oryctolagus cuniculus	Mutation(s): 0  Gene Names: Trpv5, Ecac1 Membrane Entity: Yes
UniProt
Find proteins for Q9XSM3 (Oryctolagus cuniculus) Explore Q9XSM3  Go to UniProtKB:  Q9XSM3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Calmodulin	C [auth F]	169	Bos taurus	Mutation(s): 0  Gene Names: CALM, CAM
UniProt
Find proteins for P62157 (Bos taurus) Explore P62157  Go to UniProtKB:  P62157

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cisTEM
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	Coot

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-04-24 
Deposition Author(s): Dang, S., van Goor, M.K., Asarnow, D., Wang, Y., Julius, D., Cheng, Y., van der Wijst, J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM098672
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	S10OD020054
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	S10OD021741
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R35NS105038
Netherlands Organisation for Scientific Research (NWO)	Netherlands	451001004
European Union (EU)	European Union	748058
Human Frontier Science Program (HFSP)	France	--
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2019-04-24
  Type: Initial release
  
• Version 1.1: 2019-05-15
  Changes: Data collection, Database references
• Version 1.2: 2019-11-20
  Changes: Author supporting evidence
• Version 1.3: 2019-12-18
  Changes: Other
• Version 1.4: 2024-03-20
  Changes: Data collection, Database references, Refinement description