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Yorodumi- EMDB-24636: Cryo-EM structure of the full-length TRPV1 with RTx at 4 degrees ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24636 | |||||||||
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Title | Cryo-EM structure of the full-length TRPV1 with RTx at 4 degrees Celsius, in a closed state, class I | |||||||||
Map data | 4C_RTX_closed | |||||||||
Sample |
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Function / homology | Function and homology information temperature-gated ion channel activity / response to capsazepine / excitatory extracellular ligand-gated monoatomic ion channel activity / negative regulation of establishment of blood-brain barrier / sensory perception of mechanical stimulus / peptide secretion / urinary bladder smooth muscle contraction / detection of chemical stimulus involved in sensory perception of pain / cellular response to temperature stimulus / smooth muscle contraction involved in micturition ...temperature-gated ion channel activity / response to capsazepine / excitatory extracellular ligand-gated monoatomic ion channel activity / negative regulation of establishment of blood-brain barrier / sensory perception of mechanical stimulus / peptide secretion / urinary bladder smooth muscle contraction / detection of chemical stimulus involved in sensory perception of pain / cellular response to temperature stimulus / smooth muscle contraction involved in micturition / TRP channels / cellular response to acidic pH / thermoception / fever generation / detection of temperature stimulus involved in thermoception / glutamate secretion / dendritic spine membrane / negative regulation of systemic arterial blood pressure / chloride channel regulator activity / response to pH / monoatomic cation transmembrane transporter activity / cellular response to ATP / response to pain / temperature homeostasis / negative regulation of heart rate / cellular response to alkaloid / diet induced thermogenesis / behavioral response to pain / extracellular ligand-gated monoatomic ion channel activity / intracellularly gated calcium channel activity / cellular response to cytokine stimulus / negative regulation of mitochondrial membrane potential / detection of temperature stimulus involved in sensory perception of pain / calcium ion import across plasma membrane / ligand-gated monoatomic ion channel activity / monoatomic cation channel activity / sensory perception of pain / response to organonitrogen compound / phosphatidylinositol binding / monoatomic ion transmembrane transport / cellular response to nerve growth factor stimulus / calcium ion transmembrane transport / phosphoprotein binding / microglial cell activation / calcium channel activity / lipid metabolic process / response to peptide hormone / cellular response to growth factor stimulus / positive regulation of nitric oxide biosynthetic process / calcium ion transport / transmembrane signaling receptor activity / cellular response to heat / cellular response to tumor necrosis factor / positive regulation of cytosolic calcium ion concentration / response to heat / postsynaptic membrane / protein homotetramerization / calmodulin binding / neuron projection / positive regulation of apoptotic process / external side of plasma membrane / dendrite / neuronal cell body / negative regulation of transcription by RNA polymerase II / ATP binding / membrane / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.05 Å | |||||||||
Authors | Kwon DH / Suo Y / Lee S-Y | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Vanilloid-dependent TRPV1 opening trajectory from cryoEM ensemble analysis. Authors: Do Hoon Kwon / Feng Zhang / Justin G Fedor / Yang Suo / Seok-Yong Lee / Abstract: Single particle cryo-EM often yields multiple protein conformations within a single dataset, but experimentally deducing the temporal relationship of these conformers within a conformational ...Single particle cryo-EM often yields multiple protein conformations within a single dataset, but experimentally deducing the temporal relationship of these conformers within a conformational trajectory is not trivial. Here, we use thermal titration methods and cryo-EM in an attempt to obtain temporal resolution of the conformational trajectory of the vanilloid receptor TRPV1 with resiniferatoxin (RTx) bound. Based on our cryo-EM ensemble analysis, RTx binding to TRPV1 appears to induce intracellular gate opening first, followed by selectivity filter dilation, then pore loop rearrangement to reach the final open state. This apparent conformational wave likely arises from the concerted, stepwise, additive structural changes of TRPV1 over many subdomains. Greater understanding of the RTx-mediated long-range allostery of TRPV1 could help further the therapeutic potential of RTx, which is a promising drug candidate for pain relief associated with advanced cancer or knee arthritis. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_24636.map.gz | 59.7 MB | EMDB map data format | |
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Header (meta data) | emd-24636-v30.xml emd-24636.xml | 16.5 KB 16.5 KB | Display Display | EMDB header |
Images | emd_24636.png | 65.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24636 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24636 | HTTPS FTP |
-Related structure data
Related structure data | 7rquMC 7rqvC 7rqwC 7rqxC 7rqyC 7rqzC 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_24636.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | 4C_RTX_closed | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Transient receptor potential cation channel subfamily V member 1
Entire | Name: Transient receptor potential cation channel subfamily V member 1TRPV1 |
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Components |
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-Supramolecule #1: Transient receptor potential cation channel subfamily V member 1
Supramolecule | Name: Transient receptor potential cation channel subfamily V member 1 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Recombinant expression | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 400 KDa |
-Macromolecule #1: Transient receptor potential cation channel subfamily V member 1
Macromolecule | Name: Transient receptor potential cation channel subfamily V member 1 type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 98.719758 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MEQRASLDSE ESESPPQENS CLDPPDRDPN CKPPPVKPHI FTTRSRTRLF GKGDSEEASP LDCPYEEGGL ASCPIITVSS VLTIQRPGD GPASVRPSSQ DSVSAGEKPP RLYDRRSIFD AVAQSNCQEL ESLLPFLQRS KKRLTDSEFK DPETGKTCLL K AMLNLHNG ...String: MEQRASLDSE ESESPPQENS CLDPPDRDPN CKPPPVKPHI FTTRSRTRLF GKGDSEEASP LDCPYEEGGL ASCPIITVSS VLTIQRPGD GPASVRPSSQ DSVSAGEKPP RLYDRRSIFD AVAQSNCQEL ESLLPFLQRS KKRLTDSEFK DPETGKTCLL K AMLNLHNG QNDTIALLLD VARKTDSLKQ FVNASYTDSY YKGQTALHIA IERRNMTLVT LLVENGADVQ AAANGDFFKK TK GRPGFYF GELPLSLAAC TNQLAIVKFL LQNSWQPADI SARDSVGNTV LHALVEVADN TVDNTKFVTS MYNEILILGA KLH PTLKLE EITNRKGLTP LALAASSGKI GVLAYILQRE IHEPECRHLS RKFTEWAYGP VHSSLYDLSC IDTCEKNSVL EVIA YSSSE TPNRHDMLLV EPLNRLLQDK WDRFVKRIFY FNFFVYCLYM IIFTAAAYYR PVEGLPPYKL KNTVGDYFRV TGEIL SVSG GVYFFFRGIQ YFLQRRPSLK SLFVDSYSEI LFFVQSLFML VSVVLYFSQR KEYVASMVFS LAMGWTNMLY YTRGFQ QMG IYAVMIEKMI LRDLCRFMFV YLVFLFGFST AVVTLIEDGK NNSLPMESTP HKCRGSACKP GNSYNSLYST CLELFKF TI GMGDLEFTEN YDFKAVFIIL LLAYVILTYI LLLNMLIALM GETVNKIAQE SKNIWKLQRA ITILDTEKSF LKCMRKAF R SGKLLQVGFT PDGKDDYRWC FRVDEVNWTT WNTNVGIINE DPGNCEGVKR TLSFSLRSGR VSGRNWKNFA LVPLLRDAS TRDRHATQQE EVQLKHYTGS LKPEDAEVFK DSMVPGEKEN SLEVLFQGPD YKDDDDKAHH HHHHHHHH |
-Macromolecule #2: resiniferatoxin
Macromolecule | Name: resiniferatoxin / type: ligand / ID: 2 / Number of copies: 4 / Formula: 6EU |
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Molecular weight | Theoretical: 628.708 Da |
Chemical component information | ChemComp-6EU: |
-Macromolecule #3: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
Macromolecule | Name: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / type: ligand / ID: 3 / Number of copies: 8 / Formula: LBN |
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Molecular weight | Theoretical: 760.076 Da |
Chemical component information | ChemComp-LBN: |
-Macromolecule #4: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyl...
Macromolecule | Name: [(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 |
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Molecular weight | Theoretical: 717.996 Da |
Chemical component information | ChemComp-6OU: |
-Macromolecule #5: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol
Macromolecule | Name: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol / type: ligand / ID: 5 / Number of copies: 4 / Formula: YFP |
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Molecular weight | Theoretical: 749.007 Da |
Chemical component information | ChemComp-YFP: |
-Macromolecule #6: SODIUM ION
Macromolecule | Name: SODIUM ION / type: ligand / ID: 6 / Number of copies: 2 |
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Molecular weight | Theoretical: 22.99 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.9 mg/mL | ||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY | ||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000 |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 2427 / Average exposure time: 4.0 sec. / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 2700 |
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CTF correction | Software - Name: Gctf (ver. 1.06) |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.0) |
Final 3D classification | Number classes: 2 / Software - Name: cryoSPARC |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |
Final reconstruction | Applied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 81347 |