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- PDB-8x94: Structure of human TRPV1 in complex with antagonist --protein pur... -

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Basic information

Entry
Database: PDB / ID: 8x94
TitleStructure of human TRPV1 in complex with antagonist --protein purified without CHS
ComponentsTransient receptor potential cation channel subfamily V member 1,Green fluorescent protein
KeywordsMEMBRANE 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
Transient receptor potential cation channel subfamily V member 1-4 / Transient receptor potential cation channel subfamily V / 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
CHOLESTEROL / : / Transient receptor potential cation channel subfamily V member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsFan, J. / Lei, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21625201 China
CitationJournal: 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
DepositionNov 29, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release

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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 V member 1,Green fluorescent protein
B: Transient receptor potential cation channel subfamily V member 1,Green fluorescent protein
C: Transient receptor potential cation channel subfamily V member 1,Green fluorescent protein
D: Transient receptor potential cation channel subfamily V member 1,Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)503,95912
Polymers501,1914
Non-polymers2,7688
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Transient receptor potential cation channel subfamily V member 1,Green fluorescent protein / TrpV1 / Capsaicin receptor / Osm-9-like TRP channel 1 / OTRPC1 / Vanilloid receptor 1


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.) synthetic construct (others)
Gene: TRPV1, VR1 / Production host: Homo sapiens (human) / References: UniProt: Q8NER1
#2: Chemical
ChemComp-EZI / 4-(7-Hydroxy-2-isopropyl-4-oxoquinazolin-3(4H)-yl)benzonitrile / Vanilloid receptor antagonist 1 / Libvatrep


Mass: 305.331 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H15N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H46O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: TRPV1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.36 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen 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 defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 183350 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00317752
ELECTRON MICROSCOPYf_angle_d0.51824024
ELECTRON MICROSCOPYf_dihedral_angle_d4.2092340
ELECTRON MICROSCOPYf_chiral_restr0.0362684
ELECTRON MICROSCOPYf_plane_restr0.0052956

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