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- EMDB-13037: Cryo-EM structure of the human TRPA1 ion channel in complex with ... -

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Basic information

Entry
Database: EMDB / ID: EMD-13037
TitleCryo-EM structure of the human TRPA1 ion channel in complex with the antagonist 3-60, conformation 1
Map datadensity modified map
Sample
  • Organelle or cellular component: Transient receptor potential cation channel subfamily A member 1
    • Protein or peptide: Transient receptor potential cation channel subfamily A member 1
  • Ligand: ~{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
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: CALCIUM IONCalcium
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: INOSITOL HEXAKISPHOSPHATEPhytic acid
  • Ligand: water
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 / channel activity / response to pain / cellular response to organic substance / intracellularly gated calcium channel activity / detection of mechanical stimulus involved in sensory perception of pain ...temperature-gated cation channel activity / stereocilium bundle / detection of chemical stimulus involved in sensory perception of pain / thermoception / TRP channels / channel activity / response to pain / cellular response to organic substance / 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 / response to organic substance / calcium ion transmembrane transport / calcium channel activity / intracellular calcium ion homeostasis / response to organic cyclic compound / cellular response to hydrogen peroxide / 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: 2.64 Å
AuthorsGrieben M / Pike ACW / Saward BG / Wang D / Mukhopadhyay SMM / Moreira T / Chalk R / MacLean EM / Marsden BD / Burgess-Brown NA ...Grieben M / Pike ACW / Saward BG / Wang D / Mukhopadhyay SMM / Moreira T / Chalk R / MacLean EM / Marsden BD / Burgess-Brown NA / Bountra C / Schofield CJ / Carpenter EP / Structural Genomics Consortium (SGC)
Funding support United Kingdom, 2 items
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 BG / Pike ACW / Schofield CJ / Carpenter EP
History
DepositionJun 4, 2021-
Header (metadata) releaseJun 22, 2022-
Map releaseJun 22, 2022-
UpdateJun 22, 2022-
Current statusJun 22, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13037.png

Downloads & links

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Map

FileDownload / File: emd_13037.map.gz / Format: CCP4 / Size: 80.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationdensity modified map
Voxel sizeX=Y=Z: 1.09 Å
Density
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-1.4408451 - 3.1480865
Average (Standard dev.)0.0043605743 (±0.09085099)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions276276276
Spacing276276276
CellA=B=C: 300.84 Å
α=β=γ: 90.0 °

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Supplemental data

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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
  • Organelle or cellular component: Transient receptor potential cation channel subfamily A member 1
    • Protein or peptide: Transient receptor potential cation channel subfamily A member 1
  • Ligand: ~{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
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: CALCIUM IONCalcium
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: INOSITOL HEXAKISPHOSPHATEPhytic acid
  • Ligand: water

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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: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: 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: 128.455336 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKRSLRKMWR PGEKKEPQGV VYEDVPDDTE DFKESLKVVF EGSAYGLQNF NKQKKLKTCD DMDTFFLHYA AAEGQIELME KITRDSSLE VLHEMDDYGN TPLHCAVEKN QIESVKFLLS RGANPNLRNF NMMAPLHIAV QGMNNEVMKV LLEHRTIDVN L EGENGNTA ...String:
MKRSLRKMWR PGEKKEPQGV VYEDVPDDTE DFKESLKVVF EGSAYGLQNF NKQKKLKTCD DMDTFFLHYA AAEGQIELME KITRDSSLE VLHEMDDYGN TPLHCAVEKN QIESVKFLLS RGANPNLRNF NMMAPLHIAV QGMNNEVMKV LLEHRTIDVN L EGENGNTA VIIACTTNNS EALQILLNKG AKPCKSNKWG CFPIHQAAFS GSKECMEIIL RFGEEHGYSR QLHINFMNNG KA TPLHLAV QNGDLEMIKM CLDNGAQIDP VEKGRCTAIH FAATQGATEI VKLMISSYSG SVDIVNTTDG CHETMLHRAS LFD HHELAD YLISVGADIN KIDSEGRSPL ILATASASWN IVNLLLSKGA QVDIKDNFGR NFLHLTVQQP YGLKNLRPEF MQMQ QIKEL VMDEDNDGCT PLHYACRQGG PGSVNNLLGF NVSIHSKSKD KKSPLHFAAS YGRINTCQRL LQDISDTRLL NEGDL HGMT PLHLAAKNGH DKVVQLLLKK GALFLSDHNG WTALHHASMG GYTQTMKVIL DTNLKCTDRL DEDGNTALHF AAREGH AKA VALLLSHNAD IVLNKQQASF LHLALHNKRK EVVLTIIRSK RWDECLKIFS HNSPGNKCPI TEMIEYLPEC MKVLLDF CM LHSTEDKSCR DYYIEYNFKY LQCPLEFTKK TPTQDVIYEP LTALNAMVQN NRIELLNHPV CKEYLLMKWL AYGFRAHM M NLGSYCLGLI PMTILVVNIK PGMAFNSTGI INETSDHSEI LDTTNSYLIK TCMILVFLSS IFGYCKEAGQ IFQQKRNYF MDISNVLEWI IYTTGIIFVL PLFVEIPAHL QWQCGAIAVY FYWMNFLLYL QRFENCGIFI VMLEVILKTL LRSTVVFIFL LLAFGLSFY ILLNLQDPFS SPLLSIIQTF SMMLGDINYR ESFLEPYLRN ELAHPVLSFA QLVSFTIFVP IVLMNLLIGL A VGDIAEVQ KHASLKRIAM QVELHTSLEK KLPLWFLRKV DQKSTIVYPN KPRSGGMLFH IFCFLFCTGE IRQEIPNADK SL EMEILKQ KYRLKDLTFL LEKQHELIKL IIQKMEIISE TEDDDSHCSF QDRFKKEQME QRNSRWNTVL RAVKAKTHHL EPA ENLYFQ

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Macromolecule #3: ~{N}-[4-[4-[(azanylidene-$l^{4}-azanylidene)amino]phenyl]-1,3-thi...

MacromoleculeName: ~{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
type: ligand / ID: 3 / Number of copies: 4 / Formula: 0IG
Molecular weightTheoretical: 438.443 Da
Chemical component information

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

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Macromolecule #4: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 4 / Number of copies: 8 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM / Phosphatidylcholine

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 5 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Macromolecule #7: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 7 / Number of copies: 4 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE / Phytic acid

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 52 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Average electron dose: 45.9 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 172016
FSC plot (resolution estimation)

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