6PQO

Cryo-EM structure of the human TRPA1 ion channel in complex with the covalent agonist JT010


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural Insights into Electrophile Irritant Sensing by the Human TRPA1 Channel.

Suo, Y.Wang, Z.Zubcevic, L.Hsu, A.L.He, Q.Borgnia, M.J.Ji, R.R.Lee, S.Y.

(2019) Neuron --: --

  • DOI: 10.1016/j.neuron.2019.11.023
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Transient receptor potential channel subfamily A member 1 (TRPA1) is a Ca <sup>2+ </sup>-permeable cation channel that serves as one of the primary sensors of environmental irritants and noxious substances. Many TRPA1 agonists are electrophiles that ...

    Transient receptor potential channel subfamily A member 1 (TRPA1) is a Ca 2+ -permeable cation channel that serves as one of the primary sensors of environmental irritants and noxious substances. Many TRPA1 agonists are electrophiles that are recognized by TRPA1 via covalent bond modifications of specific cysteine residues located in the cytoplasmic domains. However, a mechanistic understanding of electrophile sensing by TRPA1 has been limited due to a lack of high-resolution structural information. Here, we present the cryoelectron microscopy (cryo-EM) structures of nanodisc-reconstituted ligand-free TRPA1 and TRPA1 in complex with the covalent agonists JT010 and BITC at 2.8, 2.9, and 3.1 Å, respectively. Our structural and functional studies provide the molecular basis for electrophile recognition by the extraordinarily reactive C621 in TRPA1 and mechanistic insights into electrophile-dependent conformational changes in TRPA1. This work also provides a platform for future drug development targeting TRPA1.


    Organizational Affiliation

    Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA. Electronic address: seok-yong.lee@duke.edu.,Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA; Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA.,Center for Translational Pain Medicine, Department of Anesthesiology, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA.,Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transient receptor potential cation channel subfamily A member 1
D, A, B, C
1152Homo sapiensMutation(s): 0 
Gene Names: TRPA1 (ANKTM1)
Find proteins for O75762 (Homo sapiens)
Go to Gene View: TRPA1
Go to UniProtKB:  O75762
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JT0
Query on JT0

Download SDF File 
Download CCD File 
A, B, C, D
2-chloro-N-[4-(4-methoxyphenyl)-1,3-thiazol-2-yl]-N-(3-methoxypropyl)acetamide
C16 H19 Cl N2 O3 S
KZMAWJRXKGLWGS-UHFFFAOYSA-N
 Ligand Interaction
6OU
Query on 6OU

Download SDF File 
Download CCD File 
A, B, C, D
[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
C39 H76 N O8 P
FHQVHHIBKUMWTI-OTMQOFQLSA-N
 Ligand Interaction
LBN
Query on LBN

Download SDF File 
Download CCD File 
A, B, C, D
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
(2R)-2-[(9Z)-9-Octadecenoyloxy]-3-(palmitoyloxy)propyl 2-(trimethylammonio)ethyl phosphate
C42 H82 N O8 P
WTJKGGKOPKCXLL-VYOBOKEXSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United States--

Revision History 

  • Version 1.0: 2020-01-08
    Type: Initial release