7MBT

Cryo-EM structure of zebrafish TRPM5 E337A mutant in the presence of 5 mM calcium (low calcium occupancy in the transmembrane domain)

  • Classification: TRANSPORT PROTEIN
  • Organism(s): Danio rerio
  • Expression System: Homo sapiens
  • Mutation(s): Yes 
  • Membrane Protein: Yes  PDBTMMemProtMD

  • Deposited: 2021-04-01 Released: 2021-07-07 
  • Deposition Author(s): Ruan, Z., Lu, W., Du, J., Haley, E.
  • Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), American Heart Association

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • 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

Structures of the TRPM5 channel elucidate mechanisms of activation and inhibition.

Ruan, Z.Haley, E.Orozco, I.J.Sabat, M.Myers, R.Roth, R.Du, J.Lu, W.

(2021) Nat Struct Mol Biol 28: 604-613

  • DOI: https://doi.org/10.1038/s41594-021-00607-4
  • Primary Citation of Related Structures:  
    7MBP, 7MBQ, 7MBR, 7MBS, 7MBT, 7MBU, 7MBV

  • PubMed Abstract: 

    The Ca 2+ -activated TRPM5 channel plays essential roles in taste perception and insulin secretion. However, the mechanism by which Ca 2+ regulates TRPM5 activity remains elusive. We report cryo-EM structures of the zebrafish TRPM5 in an apo closed state, a Ca 2+ -bound open state, and an antagonist-bound inhibited state. We define two novel ligand binding sites: a Ca 2+ site (Ca ICD ) in the intracellular domain and an antagonist site in the transmembrane domain (TMD). The Ca ICD site is unique to TRPM5 and has two roles: modulating the voltage dependence and promoting Ca 2+ binding to the Ca TMD site, which is conserved throughout TRPM channels. Conformational changes initialized from both Ca 2+ sites cooperatively open the ion-conducting pore. The antagonist NDNA wedges into the space between the S1-S4 domain and pore domain, stabilizing the transmembrane domain in an apo-like closed state. Our results lay the foundation for understanding the voltage-dependent TRPM channels and developing new therapeutic agents.


  • Organizational Affiliation

    Van Andel Institute, Grand Rapids, MI, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transient receptor potential melastatin 5
A, B, C, D
1,165Danio rerioMutation(s): 1 
Gene Names: trpm5TRPM5
Membrane Entity: Yes 
UniProt
Find proteins for S5UH55 (Danio rerio)
Explore S5UH55 
Go to UniProtKB:  S5UH55
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupS5UH55
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YUY (Subject of Investigation/LOI)
Query on YUY

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C],
O [auth D]
(2R)-2-(hydroxymethyl)-4-{[(25R)-10alpha,14beta,17beta-spirost-5-en-3beta-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside
C44 H72 O15
DNENJNRTLMHVQJ-YVPDUETGSA-N
YUV (Subject of Investigation/LOI)
Query on YUV

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
M [auth C],
P [auth D]
(25R)-14beta,17beta-spirost-5-en-3beta-ol
C27 H42 O3
WQLVFSAGQJTQCK-VKROHFNGSA-N
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C],
N [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • 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 Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR56HL144929
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01NS111031
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR01HL153219
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01NS112363
American Heart AssociationUnited States20POST35120556

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-07
    Type: Initial release
  • Version 1.1: 2021-07-28
    Changes: Database references