6O6R

Structure of the TRPM8 cold receptor by single particle electron cryo-microscopy, AMTB-bound state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1126/science.aax6672
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • TRPM8 is the primary detector of environmental cold and an important target for treating pathological cold hypersensitivity. Here, we present cryo-EM structures of TRPM8 in ligand-free, antagonist- or calcium-bound forms, revealing how robust conform ...

    TRPM8 is the primary detector of environmental cold and an important target for treating pathological cold hypersensitivity. Here, we present cryo-EM structures of TRPM8 in ligand-free, antagonist- or calcium-bound forms, revealing how robust conformational changes give rise to two non-conducting states, closed and desensitized. We describe a malleable ligand-binding pocket that accommodates drugs of diverse chemical structures, and 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 Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA. yifan.cheng@ucsf.edu david.julius@ucsf.edu.,Department of Physiology, University of California, San Francisco, San Francisco, CA 94143, USA. yifan.cheng@ucsf.edu david.julius@ucsf.edu.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Physiology, University of California, San Francisco, San Francisco, CA 94143, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transient receptor potential cation channel subfamily M member 8
A, B, C, D
1098N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Y01
Query on Y01

Download SDF File 
Download CCD File 
A, B, C, D
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A, B, C, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
LQ7
Query on LQ7

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Download CCD File 
A, B, C, D
N-(3-aminopropyl)-2-[(3-methylphenyl)methoxy]-N-[(thiophen-2-yl)methyl]benzamide
C23 H26 N2 O2 S
LCQJRANJHOEQFG-UHFFFAOYSA-N
 Ligand Interaction
UND
Query on UND

Download SDF File 
Download CCD File 
A, B, C, D
UNDECANE
LIPID FRAGMENT
C11 H24
RSJKGSCJYJTIGS-UHFFFAOYSA-N
 Ligand Interaction
9PE
Query on 9PE

Download SDF File 
Download CCD File 
A, B, C, D
(1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate
3-SN-PHOSPHATIDYLETHANOLAMINE
C30 H60 N O8 P
RWBMCOYSJCETON-MUUNZHRXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2019-10-23
    Type: Data collection, Database references
  • Version 1.2: 2019-12-18
    Type: Author supporting evidence