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Yorodumi- EMDB-13036: Cryo-EM structure of the human TRPA1 ion channel in complex with ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13036 | |||||||||
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Title | Cryo-EM structure of the human TRPA1 ion channel in complex with the antagonist 3-60, conformation 2 | |||||||||
Map data | sharpened map | |||||||||
Sample |
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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 / : / 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 / : / 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 / intracellular calcium ion homeostasis / cellular response to hydrogen peroxide / protein homotetramerization / cell surface receptor signaling pathway / response to xenobiotic stimulus / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.64 Å | |||||||||
Authors | Grieben 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 | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_13036.map.gz | 41.4 MB | EMDB map data format | |
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Header (meta data) | emd-13036-v30.xml emd-13036.xml | 18.6 KB 18.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13036_fsc.xml | 9.6 KB | Display | FSC data file |
Images | emd_13036.png | 121 KB | ||
Masks | emd_13036_msk_1.map | 80.2 MB | Mask map | |
Others | emd_13036_half_map_1.map.gz emd_13036_half_map_2.map.gz | 74 MB 74 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13036 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13036 | HTTPS FTP |
-Validation report
Summary document | emd_13036_validation.pdf.gz | 767.9 KB | Display | EMDB validaton report |
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Full document | emd_13036_full_validation.pdf.gz | 767.5 KB | Display | |
Data in XML | emd_13036_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | emd_13036_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13036 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13036 | HTTPS FTP |
-Related structure data
Related structure data | 7or0MC 7or1C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_13036.map.gz / Format: CCP4 / Size: 80.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_13036_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half A
File | emd_13036_half_map_1.map | ||||||||||||
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Annotation | half A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half B
File | emd_13036_half_map_2.map | ||||||||||||
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Annotation | half B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Transient receptor potential cation channel subfamily A member 1
Entire | Name: Transient receptor potential cation channel subfamily A member 1 |
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Components |
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-Supramolecule #1: Transient receptor potential cation channel subfamily A member 1
Supramolecule | Name: Transient receptor potential cation channel subfamily A member 1 type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-Macromolecule #1: Transient receptor potential cation channel subfamily A member 1
Macromolecule | Name: Transient receptor potential cation channel subfamily A member 1 type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 128.455336 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #3: ~{N}-[4-[4-[(azanylidene-$l^{4}-azanylidene)amino]phenyl]-1,3-thi...
Macromolecule | Name: ~{N}-[4-[4-[(azanylidene-$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 |
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Molecular weight | Theoretical: 438.443 Da |
Chemical component information | ChemComp-0IG: |
-Macromolecule #4: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Macromolecule | Name: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 4 / Number of copies: 8 / Formula: PC1 |
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Molecular weight | Theoretical: 790.145 Da |
Chemical component information | ChemComp-PC1: |
-Macromolecule #5: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 5 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 4 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Macromolecule #7: INOSITOL HEXAKISPHOSPHATE
Macromolecule | Name: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 7 / Number of copies: 4 / Formula: IHP |
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Molecular weight | Theoretical: 660.035 Da |
Chemical component information | ChemComp-IHP: |
-Macromolecule #8: water
Macromolecule | Name: water / type: ligand / ID: 8 / Number of copies: 52 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Average electron dose: 45.9 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |