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- EMDB-20450: Cryo-EM structure of the human TRPA1 ion channel in complex with ... -

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Basic information

Entry
Database: EMDB / ID: EMD-20450
TitleCryo-EM structure of the human TRPA1 ion channel in complex with the covalent agonist BITC
Map dataFull map
Sample
  • Complex: Transient receptor potential cation channel subfamily A member 1
    • Protein or peptide: Transient receptor potential cation channel subfamily A member 1
  • Ligand: N-benzylthioformamide
  • Ligand: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
KeywordsIon channel / TRP channel / TRPA channel / TRPA1 channel / irritant sensing / BITC / membrane protein / TRANSPORT PROTEIN
Function / homology
Function and homology information


temperature-gated cation channel activity / stereocilium bundle / detection of chemical stimulus involved in sensory perception of pain / thermoception / TRP channels / response to pain / intracellularly gated calcium channel activity / detection of mechanical stimulus involved in sensory perception of pain / monoatomic ion transport / sensory perception of pain ...temperature-gated cation channel activity / stereocilium bundle / detection of chemical stimulus involved in sensory perception of pain / thermoception / TRP channels / response to pain / intracellularly gated calcium channel activity / detection of mechanical stimulus involved in sensory perception of pain / monoatomic ion transport / sensory perception of pain / response to cold / calcium ion transmembrane transport / calcium channel activity / response to organic cyclic compound / cellular response to hydrogen peroxide / intracellular calcium ion homeostasis / channel activity / protein homotetramerization / cell surface receptor signaling pathway / response to xenobiotic stimulus / identical protein binding / plasma membrane
Similarity search - Function
: / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Transient receptor potential cation channel subfamily A member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsSuo Y / Wang Z
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) United States
CitationJournal: Neuron / Year: 2020
Title: Structural Insights into Electrophile Irritant Sensing by the Human TRPA1 Channel.
Authors: Yang Suo / Zilong Wang / Lejla Zubcevic / Allen L Hsu / Qianru He / Mario J Borgnia / Ru-Rong Ji / Seok-Yong Lee /
Abstract: Transient receptor potential channel subfamily A member 1 (TRPA1) is a Ca-permeable cation channel that serves as one of the primary sensors of environmental irritants and noxious substances. Many ...Transient receptor potential channel subfamily A member 1 (TRPA1) is a Ca-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.
History
DepositionJul 9, 2019-
Header (metadata) releaseSep 18, 2019-
Map releaseJan 8, 2020-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6pqp
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20450.png

Downloads & links

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Map

FileDownload / File: emd_20450.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 272.896 Å		1.07 Å/pix.
x 256 pix.
= 272.896 Å		1.07 Å/pix.
x 256 pix.
= 272.896 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.066 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.056339625 - 0.08403988
Average (Standard dev.)0.0000122815645 (±0.002908765)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-25600
Dimensions256256256
Spacing256256256
CellA=B=C: 272.896 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0661.0661.066
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z272.896272.896272.896
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS0-2560
NC/NR/NS256256256
D min/max/mean-0.0560.0840.000

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Supplemental data

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Half map: half map 1

Fileemd_20450_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_20450_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Transient receptor potential cation channel subfamily A member 1

EntireName: Transient receptor potential cation channel subfamily A member 1
Components
  • Complex: Transient receptor potential cation channel subfamily A member 1
    • Protein or peptide: Transient receptor potential cation channel subfamily A member 1
  • Ligand: N-benzylthioformamide
  • Ligand: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine

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Supramolecule #1: Transient receptor potential cation channel subfamily A member 1

SupramoleculeName: Transient receptor potential cation channel subfamily A member 1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Transient receptor potential cation channel subfamily A member 1

MacromoleculeName: Transient receptor potential cation channel subfamily A member 1
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 131.495547 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAKRSLRKMW RPGEKKEPQG VVYEDVPDDT EDFKESLKVV FEGSAYGLQN FNKQKKLKRC DDMDTFFLHY AAAEGQIELM EKITRDSSL EVLHEMDDYG NTPLHCAVEK NQIESVKFLL SRGANPNLRN FNMMAPLHIA VQGMNNEVMK VLLEHRTIDV N LEGENGNT ...String:
MAKRSLRKMW RPGEKKEPQG VVYEDVPDDT EDFKESLKVV FEGSAYGLQN FNKQKKLKRC DDMDTFFLHY AAAEGQIELM EKITRDSSL EVLHEMDDYG NTPLHCAVEK NQIESVKFLL SRGANPNLRN FNMMAPLHIA VQGMNNEVMK VLLEHRTIDV N LEGENGNT AVIIACTTNN SEALQILLKK GAKPCKSNKW GCFPIHQAAF SGSKECMEII LRFGEEHGYS RQLHINFMNN GK ATPLHLA VQNGDLEMIK MCLDNGAQID PVEKGRCTAI HFAATQGATE IVKLMISSYS GSVDIVNTTD GCHETMLHRA SLF DHHELA DYLISVGADI NKIDSEGRSP LILATASASW NIVNLLLSKG AQVDIKDNFG RNFLHLTVQQ PYGLKNLRPE FMQM QQIKE LVMDEDNDGC TPLHYACRQG GPGSVNNLLG FNVSIHSKSK DKKSPLHFAA SYGRINTCQR LLQDISDTRL LNEGD LHGM TPLHLAAKNG HDKVVQLLLK KGALFLSDHN GWTALHHASM GGYTQTMKVI LDTNLKCTDR LDEDGNTALH FAAREG HAK AVALLLSHNA DIVLNKQQAS FLHLALHNKR KEVVLTIIRS KRWDECLKIF SHNSPGNKCP ITEMIEYLPE CMKVLLD FC MLHSTEDKSC RDYYIEYNFK YLQCPLEFTK KTPTQDVIYE PLTALNAMVQ NNRIELLNHP VCKEYLLMKW LAYGFRAH M MNLGSYCLGL IPMTILVVNI KPGMAFNSTG IINETSDHSE ILDTTNSYLI KTCMILVFLS SIFGYCKEAG QIFQQKRNY FMDISNVLEW IIYTTGIIFV LPLFVEIPAH LQWQCGAIAV YFYWMNFLLY LQRFENCGIF IVMLEVILKT LLRSTVVFIF LLLAFGLSF YILLNLQDPF SSPLLSIIQT FSMMLGDINY RESFLEPYLR NELAHPVLSF AQLVSFTIFV PIVLMNLLIG L AVGDIAEV QKHASLKRIA MQVELHTSLE KKLPLWFLRK VDQKSTIVYP NKPRSGGMLF HIFCFLFCTG EIRQEIPNAD KS LEMEILK QKYRLKDLTF LLEKQHELIK LIIQKMEIIS ETEDDDSHCS FQDRFKKEQM EQRNSRWNTV LRAVKAKTHH LEP SNSLEV LFQGPAADYK DDDDKAHHHH HHHHHH

UniProtKB: Transient receptor potential cation channel subfamily A member 1

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Macromolecule #3: N-benzylthioformamide

MacromoleculeName: N-benzylthioformamide / type: ligand / ID: 3 / Number of copies: 4 / Formula: 9BE
Molecular weightTheoretical: 151.229 Da
Chemical component information

ChemComp-9BE:
N-benzylthioformamide

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Macromolecule #4: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyl...

MacromoleculeName: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
type: ligand / ID: 4 / Number of copies: 20 / Formula: 6OU
Molecular weightTheoretical: 717.996 Da
Chemical component information

ChemComp-6OU:
[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate / phospholipid*YM

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Macromolecule #5: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine

MacromoleculeName: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / type: ligand / ID: 5 / Number of copies: 4 / Formula: LBN
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-LBN:
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / phospholipid*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 8
GridModel: UltrAuFoil / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 26 sec. / Details: 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 4418 / Average exposure time: 4.6 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.25 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 396597
Startup modelType of model: OTHER
Details: The TRPA1 in complex with covalent agonist JT010 structure (reported in the same study) was low-pass filtered to 30 Angstrom and used as initial model.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 74677
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.0)

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Atomic model buiding 1

Initial modelPDB ID:

3j9p


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 100
Output model

PDB-6pqp:
Cryo-EM structure of the human TRPA1 ion channel in complex with the covalent agonist BITC

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