6O6R

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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:  
    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 ...

    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. yifan.cheng@ucsf.edu david.julius@ucsf.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transient receptor potential cation channel subfamily M member 8A, B, C, D1,098Parus majorMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9PE
Query on 9PE

Download Ideal Coordinates CCD File 
BA [auth D],
G [auth A],
N [auth B],
U [auth C]
(1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate
C30 H60 N O8 P
RWBMCOYSJCETON-MUUNZHRXSA-N
 Ligand Interaction
Y01
Query on Y01

Download Ideal Coordinates CCD File 
E [auth A],
L [auth B],
S [auth C],
Z [auth D]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
 Ligand Interaction
LQ7
Query on LQ7

Download Ideal Coordinates CCD File 
DA [auth D],
I [auth A],
P [auth B],
W [auth C]
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 Ideal Coordinates CCD File 
AA [auth D],
CA [auth D],
F [auth A],
H [auth A],
M [auth B],
AA [auth D],
CA [auth D],
F [auth A],
H [auth A],
M [auth B],
O [auth B],
T [auth C],
V [auth C]
UNDECANE
C11 H24
RSJKGSCJYJTIGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
EA [auth D],
FA [auth D],
J [auth A],
K [auth A],
Q [auth B],
EA [auth D],
FA [auth D],
J [auth A],
K [auth A],
Q [auth B],
R [auth B],
X [auth C],
Y [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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: 2019-10-23
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence