9B90

Cryo-EM structure of the human TRPM4 channel in complex with calcium and ATP at 37 degrees Celsius

  • Classification: MEMBRANE PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Mammalia
  • Mutation(s): No 
  • Membrane Protein: Yes  PDBTM

  • Deposited: 2024-04-01 Released: 2024-05-15 
  • Deposition Author(s): Hu, J., Lu, W., Du, J.
  • 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), Other private, American Heart Association

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 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

Physiological temperature drives TRPM4 ligand recognition and gating.

Hu, J.Park, S.J.Walter, T.Orozco, I.J.O'Dea, G.Ye, X.Du, J.Lu, W.

(2024) Nature 

  • DOI: https://doi.org/10.1038/s41586-024-07436-7
  • Primary Citation of Related Structures:  
    9B8W, 9B8X, 9B8Y, 9B8Z, 9B90, 9B91, 9B92, 9B93, 9B94

  • PubMed Abstract: 

    Temperature profoundly affects macromolecular function, particularly in proteins with temperature sensitivity 1,2 . However, its impact is often overlooked in biophysical studies that are typically performed at non-physiological temperatures, potentially leading to inaccurate mechanistic and pharmacological insights. Here we demonstrate temperature-dependent changes in the structure and function of TRPM4, a temperature-sensitive Ca 2+ -activated ion channel 3-7 . By studying TRPM4 prepared at physiological temperature using single-particle cryo-electron microscopy, we identified a 'warm' conformation that is distinct from those observed at lower temperatures. This conformation is driven by a temperature-dependent Ca 2+ -binding site in the intracellular domain, and is essential for TRPM4 function in physiological contexts. We demonstrated that ligands, exemplified by decavanadate (a positive modulator) 8 and ATP (an inhibitor) 9 , bind to different locations of TRPM4 at physiological temperatures than at lower temperatures 10,11 , and that these sites have bona fide functional relevance. We elucidated the TRPM4 gating mechanism by capturing structural snapshots of its different functional states at physiological temperatures, revealing the channel opening that is not observed at lower temperatures. Our study provides an example of temperature-dependent ligand recognition and modulation of an ion channel, underscoring the importance of studying macromolecules at physiological temperatures. It also provides a potential molecular framework for deciphering how thermosensitive TRPM channels perceive temperature changes.


  • 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 cation channel subfamily M member 4
A, B, C, D
1,214Homo sapiensMutation(s): 0 
Gene Names: TRPM4LTRPC4
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TD43 (Homo sapiens)
Explore Q8TD43 
Go to UniProtKB:  Q8TD43
PHAROS:  Q8TD43
GTEx:  ENSG00000130529 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TD43
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
M [auth C],
P [auth D]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
H [auth B]
I [auth B]
K [auth C]
E [auth A],
F [auth A],
H [auth B],
I [auth B],
K [auth C],
L [auth C],
N [auth D],
O [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 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 Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR01HL153219
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01NS129804
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01NS111031
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01NS112363
Other privateMcKnight Scholar Award
Other privateKlingenstein-Simon Scholar Award
Other privateSloan Research Fellowship
Other privatePew Scholar in the Biomedical Sciences
American Heart AssociationUnited States24POST1196982

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-15
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Database references