6O6A | pdb_00006o6a

Structure of the TRPM8 cold receptor by single particle electron cryo-microscopy, ligand-free state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6O6A

This is version 1.4 of the entry. See complete history

Literature

Structural insights into TRPM8 inhibition and desensitization.

Diver, M.M.Cheng, Y.Julius, D.

(2019) Science 365: 1434-1440

  • DOI: https://doi.org/10.1126/science.aax6672
  • Primary Citation Related Structures: 
    6O6A, 6O6R, 6O72, 6O77

  • PubMed Abstract: 

    The transient receptor potential melastatin 8 (TRPM8) ion channel is the primary detector of environmental cold and an important target for treating pathological cold hypersensitivity. Here, we present cryo-electron microscopy structures of TRPM8 in ligand-free, antagonist-bound, or calcium-bound forms, revealing how robust conformational changes give rise to two nonconducting states, closed and desensitized. We describe a malleable ligand-binding pocket that accommodates drugs of diverse chemical structures, and we delineate the ion permeation pathway, including the contribution of lipids to pore architecture. Furthermore, we show that direct calcium binding mediates stimulus-evoked desensitization, clarifying this important mechanism of sensory adaptation. We observe large rearrangements within the S4-S5 linker that reposition the S1-S4 and pore domains relative to the TRP helix, leading us to propose a distinct model for modulation of TRPM8 and possibly other TRP channels.


  • Organizational Affiliation
    • Department of Physiology, University of California, San Francisco, San Francisco, CA 94143, USA.

Macromolecule Content 

  • Total Structure Weight: 510 kDa 
  • Atom Count: 27,220 
  • Modeled Residue Count: 3,312 
  • Deposited Residue Count: 4,392 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transient receptor potential cation channel subfamily M member 8
A, B, C, D
1,098Parus majorMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A5S8WF66 (Parus major)
Explore A0A5S8WF66 
Go to UniProtKB:  A0A5S8WF66
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5S8WF66
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y01

Query on Y01



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
I [auth C],
K [auth D]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
F [auth A],
H [auth B],
J [auth C],
L [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 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 Human Genome Research Institute (NIH/NHGRI)United StatesR35NS105038
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesR01GM098672
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesS10OD020054
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesS10OD021741

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2019-09-25
    Changes: Data collection, Data processing
  • Version 1.2: 2019-10-23
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.4: 2024-03-20
    Changes: Data collection, Database references