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- PDB-7or1: Cryo-EM structure of the human TRPA1 ion channel in complex with ... -

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Basic information

Entry
Database: PDB / ID: 7or1
TitleCryo-EM structure of the human TRPA1 ion channel in complex with the antagonist 3-60, conformation 1
ComponentsTransient receptor potential cation channel subfamily A member 1
KeywordsMEMBRANE PROTEIN / Transient receptor potential cation channel subfamily A member 1 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


regulation of blood circulation / positive regulation of monoatomic anion transport / cellular response to food / temperature-gated cation channel activity / regulation of neuronal action potential / cellular response to carbon dioxide / osmolarity-sensing monoatomic cation channel activity / stereocilium bundle / detection of chemical stimulus involved in sensory perception of pain / urinary bladder smooth muscle contraction ...regulation of blood circulation / positive regulation of monoatomic anion transport / cellular response to food / temperature-gated cation channel activity / regulation of neuronal action potential / cellular response to carbon dioxide / osmolarity-sensing monoatomic cation channel activity / stereocilium bundle / detection of chemical stimulus involved in sensory perception of pain / urinary bladder smooth muscle contraction / thermoception / cellular response to toxic substance / cellular response to caffeine / response to pain / calcium ion transmembrane import into cytosol / TRP channels / cellular response to cold / intracellularly gated calcium channel activity / detection of mechanical stimulus involved in sensory perception of pain / positive regulation of insulin secretion involved in cellular response to glucose stimulus / voltage-gated calcium channel activity / monoatomic ion transport / sensory perception of pain / response to cold / calcium ion transmembrane transport / calcium channel activity / cellular response to hydrogen peroxide / intracellular calcium ion homeostasis / cellular response to heat / channel activity / protein homotetramerization / cell surface receptor signaling pathway / apical plasma membrane / response to xenobiotic stimulus / axon / 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
Chem-0IG / INOSITOL HEXAKISPHOSPHATE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Transient receptor potential cation channel subfamily A member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.64 Å
AuthorsGrieben, M. / Pike, A.C.W. / Saward, B.G. / Wang, D. / Mukhopadhyay, S.M.M. / Moreira, T. / Chalk, R. / MacLean, E.M. / Marsden, B.D. / Burgess-Brown, N.A. ...Grieben, M. / Pike, A.C.W. / Saward, B.G. / Wang, D. / Mukhopadhyay, S.M.M. / Moreira, T. / Chalk, R. / MacLean, E.M. / Marsden, B.D. / Burgess-Brown, N.A. / Bountra, C. / Schofield, C.J. / Carpenter, E.P. / Structural Genomics Consortium (SGC)
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust106169/Z/14/Z United Kingdom
European Commission115766 United Kingdom
CitationJournal: TO BE PUBLISHED
Title: Cryo-EM structure of the human TRPA1 ion channel in complex with the antagonist 3-60
Authors: Grieben, M. / Saward, B.G. / Pike, A.C.W. / Schofield, C.J. / Carpenter, E.P.
History
DepositionJun 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transient receptor potential cation channel subfamily A member 1
B: Transient receptor potential cation channel subfamily A member 1
C: Transient receptor potential cation channel subfamily A member 1
D: Transient receptor potential cation channel subfamily A member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)527,31933
Polymers513,8214
Non-polymers13,49829
Water93752
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LYSGLUA1 - 596
d_12ens_1CS1CS1A1
d_13ens_1IHPIHPA
d_14ens_1PC1PC1A
d_15ens_1PC1PC1A
d_16ens_1CACAA
d_17ens_1NAGNAGA
d_18ens_1NAGNAGA
d_19ens_1NAGNAGA
d_21ens_1LYSGLUB1 - 596
d_22ens_1CS1CS1B1
d_23ens_1IHPIHPB
d_24ens_1PC1PC1B
d_25ens_1PC1PC1B
d_26ens_1CACAB
d_27ens_1NAGNAGB
d_28ens_1NAGNAGB
d_29ens_1NAGNAGB
d_31ens_1LYSGLUC1 - 596
d_32ens_1CS1CS1C1
d_33ens_1IHPIHPC
d_34ens_1PC1PC1C
d_35ens_1PC1PC1C
d_36ens_1CACAC
d_37ens_1NAGNAGC
d_38ens_1NAGNAGC
d_39ens_1NAGNAGC
d_41ens_1LYSGLUD1 - 596
d_42ens_1CS1CS1D1
d_43ens_1IHPIHPD
d_44ens_1PC1PC1D
d_45ens_1PC1PC1D
d_46ens_1CACAD
d_47ens_1NAGNAGD
d_48ens_1NAGNAGD
d_49ens_1NAGNAGD

NCS oper:
IDCodeMatrixVector
1given(-0.00540010790894, 0.999983341331, 0.00203860146879), (-0.99998529821, -0.00540109933469, 0.000481134682618), (0.000492137356591, -0.0020359733185, 0.999997806304)0.447541865625, 301.513700881, 0.437422818324
2given(-0.999995431212, -0.00229542122124, -0.0019668746637), (0.00229304751777, -0.999996641031, 0.00120824661918), (-0.00196964149196, 0.00120373096189, 0.999997335769)301.635018713, 300.222704681, 0.136263123055
3given(0.00565982105031, -0.999982801975, 0.00153693833075), (0.999983259592, 0.0056616591089, 0.00119421639391), (-0.00120289747664, 0.00153015355069, 0.999998105832)299.781252496, -1.11762833758, -0.0804972979273

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Transient receptor potential cation channel subfamily A member 1 / Ankyrin-like with transmembrane domains protein 1 / Transformation-sensitive protein p120 / Wasabi receptor


Mass: 128455.336 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRPA1, ANKTM1 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: O75762

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Sugars , 2 types, 8 molecules

#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 73 molecules

#3: Chemical
ChemComp-0IG / ~{N}-[4-[4-[(azanylidene-$l^{4}-azanylidene)amino]phenyl]-1,3-thiazol-2-yl]-2-[1,3-dimethyl-2,6-bis(oxidanylidene)purin-7-yl]ethanamide


Mass: 438.443 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H16N9O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C44H88NO8P / Comment: phospholipid*YM
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#7: Chemical
ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H18O24P6
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Transient receptor potential cation channel subfamily A member 1
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 1400 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 45.9 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.19.1_4122refinement
PHENIX1.19.1_4122refinement
EM software
IDNameCategory
1RELIONparticle selection
2EPUimage acquisition
4RELIONCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 172016 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 92.73 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007320236
ELECTRON MICROSCOPYf_angle_d0.575527412
ELECTRON MICROSCOPYf_chiral_restr0.04343164
ELECTRON MICROSCOPYf_plane_restr0.00453420
ELECTRON MICROSCOPYf_dihedral_angle_d13.24127620
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AELECTRON MICROSCOPYNCS constraints0.000709213030947
ens_1d_3AELECTRON MICROSCOPYNCS constraints0.000712394281674
ens_1d_4AELECTRON MICROSCOPYNCS constraints0.000706221819218

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