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- EMDB-65639: Structure of rat TRPV1 in complex with SB-366791 -

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Basic information

Entry
Database: EMDB / ID: EMD-65639
TitleStructure of rat TRPV1 in complex with SB-366791
Map data
Sample
  • Complex: Cryo-EM structure of rat TRPV1 in complex with the analgesic drug SB-36679
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 1
  • Ligand: (2E)-3-(4-chlorophenyl)-N-(3-methoxyphenyl)prop-2-enamide
KeywordsTRPV1 / protein complex / TRANSPORT PROTEIN
Function / homology
Function and homology information


negative regulation of iodide transmembrane transport / positive regulation of membrane depolarization / negative regulation of establishment of blood-brain barrier / response to capsazepine / sensory perception of mechanical stimulus / peptide secretion / cellular response to temperature stimulus / positive regulation of sensory perception of pain / temperature-gated ion channel activity / detection of chemical stimulus involved in sensory perception of pain ...negative regulation of iodide transmembrane transport / positive regulation of membrane depolarization / negative regulation of establishment of blood-brain barrier / response to capsazepine / sensory perception of mechanical stimulus / peptide secretion / cellular response to temperature stimulus / positive regulation of sensory perception of pain / temperature-gated ion channel activity / detection of chemical stimulus involved in sensory perception of pain / positive regulation of renal sodium excretion / negative regulation of axon regeneration / TRP channels / positive regulation of cardiac muscle cell differentiation / smooth muscle contraction involved in micturition / fever generation / detection of temperature stimulus involved in thermoception / thermoception / urinary bladder smooth muscle contraction / response to pH / monoatomic cation transmembrane transporter activity / glutamate secretion / negative regulation of systemic arterial blood pressure / dendritic spine membrane / positive regulation of urine volume / excitatory extracellular ligand-gated monoatomic ion channel activity / negative regulation of heart rate / response to acidic pH / response to pain / diet induced thermogenesis / cellular response to alkaloid / cellular response to cytokine stimulus / temperature homeostasis / cellular response to ATP / intracellularly gated calcium channel activity / detection of temperature stimulus involved in sensory perception of pain / negative regulation of mitochondrial membrane potential / behavioral response to pain / calcium ion import across plasma membrane / positive regulation of vasoconstriction / monoatomic ion channel activity / ligand-gated monoatomic ion channel activity / monoatomic cation channel activity / cellular response to acidic pH / extracellular ligand-gated monoatomic ion channel activity / phosphatidylinositol binding / sensory perception of pain / axon terminus / positive regulation of excitatory postsynaptic potential / sarcoplasmic reticulum / lipid metabolic process / phosphoprotein binding / microglial cell activation / cellular response to nerve growth factor stimulus / response to peptide hormone / cellular response to growth factor stimulus / GABA-ergic synapse / calcium ion transmembrane transport / cellular response to tumor necrosis factor / calcium channel activity / positive regulation of nitric oxide biosynthetic process / calcium ion transport / transmembrane signaling receptor activity / cellular response to heat / sensory perception of taste / response to heat / positive regulation of cytosolic calcium ion concentration / monoatomic ion transmembrane transport / protein homotetramerization / calmodulin binding / postsynaptic membrane / neuron projection / positive regulation of apoptotic process / external side of plasma membrane / neuronal cell body / dendrite / negative regulation of transcription by RNA polymerase II / ATP binding / membrane / metal ion binding / identical protein binding / nucleus / 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
Transient receptor potential cation channel subfamily V member 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsChen X / Yu Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371289 China
CitationJournal: To Be Published
Title: Cryo-EM structure of rat TRPV1 in complex with the analgesic drug SB-36679
Authors: Yu Y
History
DepositionJul 31, 2025-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65639.png

Downloads & links

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Map

FileDownload / File: emd_65639.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.107
Minimum - Maximum-0.54918504 - 0.8147074
Average (Standard dev.)0.0012552629 (±0.028171543)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 238.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65639_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65639_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of rat TRPV1 in complex with the analgesic drug...

EntireName: Cryo-EM structure of rat TRPV1 in complex with the analgesic drug SB-36679
Components
  • Complex: Cryo-EM structure of rat TRPV1 in complex with the analgesic drug SB-36679
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 1
  • Ligand: (2E)-3-(4-chlorophenyl)-N-(3-methoxyphenyl)prop-2-enamide

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Supramolecule #1: Cryo-EM structure of rat TRPV1 in complex with the analgesic drug...

SupramoleculeName: Cryo-EM structure of rat TRPV1 in complex with the analgesic drug SB-36679
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: Transient receptor potential cation channel subfamily V member 1

MacromoleculeName: Transient receptor potential cation channel subfamily V member 1
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 99.514625 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DYKDDDDKWS HPQFEKGGGG SGGSAWSHPQ FEKEFKGLVD MEQRASLDSE ESESPPQENS CLDPPDRDPN CKPPPVKPHI FTTRSRTRL FGKGDSEEAS PLDCPYEEGG LASCPIITVS SVLTIQRPGD GPASVRPSSQ DSVSAGEKPP RLYDRRSIFD A VAQSNCQE ...String:
DYKDDDDKWS HPQFEKGGGG SGGSAWSHPQ FEKEFKGLVD MEQRASLDSE ESESPPQENS CLDPPDRDPN CKPPPVKPHI FTTRSRTRL FGKGDSEEAS PLDCPYEEGG LASCPIITVS SVLTIQRPGD GPASVRPSSQ DSVSAGEKPP RLYDRRSIFD A VAQSNCQE LESLLPFLQR SKKRLTDSEF KDPETGKTCL LKAMLNLHNG QNDTIALLLD VARKTDSLKQ FVNASYTDSY YK GQTALHI AIERRNMTLV TLLVENGADV QAAANGDFFK KTKGRPGFYF GELPLSLAAC TNQLAIVKFL LQNSWQPADI SAR DSVGNT VLHALVEVAD NTVDNTKFVT SMYNEILILG AKLHPTLKLE EITNRKGLTP LALAASSGKI GVLAYILQRE IHEP ECRHL SRKFTEWAYG PVHSSLYDLS CIDTCEKNSV LEVIAYSSSE TPNRHDMLLV EPLNRLLQDK WDRFVKRIFY FNFFV YCLY MIIFTAAAYY RPVEGLPPYK LKNTVGDYFR VTGEILSVSG GVYFFFRGIQ YFLQRRPSLK SLFVDSYSEI LFFVQS LFM LVSVVLYFSQ RKEYVASMVF SLAMGWTNML YYTRGFQQMG IYAVMIEKMI LRDLCRFMFV YLVFLFGFST AVVTLIE DG KNNSLPMEST PHKCRGSACK PGNSYNSLYS TCLELFKFTI GMGDLEFTEN YDFKAVFIIL LLAYVILTYI LLLNMLIA L MGETVNKIAQ ESKNIWKLQR AITILDTEKS FLKCMRKAFR SGKLLQVGFT PDGKDDYRWC FRVDEVNWTT WNTNVGIIN EDPGNCEGVK RTLSFSLRSG RVSGRNWKNF ALVPLLRDAS TRDRHATQQE EVQLKHYTGS LKPEDAEVFK DSMVPGEK

UniProtKB: Transient receptor potential cation channel subfamily V member 1

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Macromolecule #2: (2E)-3-(4-chlorophenyl)-N-(3-methoxyphenyl)prop-2-enamide

MacromoleculeName: (2E)-3-(4-chlorophenyl)-N-(3-methoxyphenyl)prop-2-enamide
type: ligand / ID: 2 / Number of copies: 4 / Formula: ZEI
Molecular weightTheoretical: 287.741 Da
Chemical component information

ChemComp-ZEI:
(2E)-3-(4-chlorophenyl)-N-(3-methoxyphenyl)prop-2-enamide

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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: 8 / Details: 20 mM Hepes, 150 mM NaCl
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 4.5 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 15491
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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