+Open data
-Basic information
Entry | Database: PDB / ID: 8jqr | ||||||
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Title | Structure of human TRPV1 in complex with antagonist | ||||||
Components | Transient receptor potential cation channel subfamily V member 1,PreScission Site,Green fluorescent protein | ||||||
Keywords | MEMBRANE PROTEIN / channel | ||||||
Function / homology | Function and homology information chemosensory behavior / temperature-gated ion channel activity / response to capsazepine / negative regulation of establishment of blood-brain barrier / sensory perception of mechanical stimulus / peptide secretion / detection of chemical stimulus involved in sensory perception of pain / smooth muscle contraction involved in micturition / cellular response to temperature stimulus / cellular response to acidic pH ...chemosensory behavior / temperature-gated ion channel activity / response to capsazepine / negative regulation of establishment of blood-brain barrier / sensory perception of mechanical stimulus / peptide secretion / detection of chemical stimulus involved in sensory perception of pain / smooth muscle contraction involved in micturition / cellular response to temperature stimulus / cellular response to acidic pH / excitatory extracellular ligand-gated monoatomic ion channel activity / fever generation / thermoception / detection of temperature stimulus involved in thermoception / glutamate secretion / negative regulation of systemic arterial blood pressure / chloride channel regulator activity / dendritic spine membrane / TRP channels / cellular response to ATP / negative regulation of heart rate / cellular response to alkaloid / calcium ion import across plasma membrane / diet induced thermogenesis / behavioral response to pain / intracellularly gated calcium channel activity / detection of temperature stimulus involved in sensory perception of pain / negative regulation of mitochondrial membrane potential / voltage-gated calcium channel activity / extracellular ligand-gated monoatomic ion channel activity / phosphatidylinositol binding / cellular response to nerve growth factor stimulus / lipid metabolic process / phosphoprotein binding / calcium ion transmembrane transport / microglial cell activation / calcium channel activity / transmembrane signaling receptor activity / response to peptide hormone / positive regulation of nitric oxide biosynthetic process / cellular response to tumor necrosis factor / positive regulation of cytosolic calcium ion concentration / cellular response to heat / postsynaptic membrane / protein homotetramerization / cell surface receptor signaling pathway / calmodulin binding / positive regulation of apoptotic process / external side of plasma membrane / neuronal cell body / negative regulation of transcription by RNA polymerase II / ATP binding / identical protein binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Pseudotevenvirus RB43 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 Å | ||||||
Authors | Fan, J. / Lei, X. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: Structural basis of TRPV1 inhibition by SAF312 and cholesterol Authors: Fan, J. / Ke, H. / Lei, J. / Wang, J. / Tominaga, M. / Lei, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jqr.cif.gz | 419.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jqr.ent.gz | 321.5 KB | Display | PDB format |
PDBx/mmJSON format | 8jqr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jqr_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8jqr_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8jqr_validation.xml.gz | 66.7 KB | Display | |
Data in CIF | 8jqr_validation.cif.gz | 96.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jq/8jqr ftp://data.pdbj.org/pub/pdb/validation_reports/jq/8jqr | HTTPS FTP |
-Related structure data
Related structure data | 36577MC 8x94C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 125297.734 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: The section (840-842) is the cloning site.The domain (843-850) is PreScission Site.The domain (851-1084) is corresponding to this sfGFP (462-695 amino acids, GenBank: ALP48449.1). The domain ...Details: The section (840-842) is the cloning site.The domain (843-850) is PreScission Site.The domain (851-1084) is corresponding to this sfGFP (462-695 amino acids, GenBank: ALP48449.1). The domain (1085-1112) is the expression Tag. Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Pseudotevenvirus RB43 Gene: TRPV1, VR1 / Production host: Homo sapiens (human) / References: UniProt: Q8NER1 #2: Chemical | ChemComp-EZI / Mass: 305.331 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H15N3O2 / Feature type: SUBJECT OF INVESTIGATION #3: Chemical | ChemComp-CLR / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: TRPV1 / Type: COMPLEX / Entity ID: #1 / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 0.36 MDa / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293 |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 239934 / Symmetry type: POINT | ||||||||||||||||||||||||
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