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- EMDB-60835: Structure of rat TRPV1 in complex with PSFL426-S5 -

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Basic information

Entry
Database: EMDB / ID: EMD-60835
TitleStructure of rat TRPV1 in complex with PSFL426-S5
Map data
Sample
  • Complex: Structure of rat TRPV1 in complex with PSFL426-S5
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 1
  • Ligand: 4-azanyl-3-sulfanylidene-1,2,4-triazine-5,6-dione
KeywordsTRPV1 / protein complex / MEMBRANE PROTEIN
Function / homology
Function and homology information


negative regulation of establishment of blood-brain barrier / response to capsazepine / sensory perception of mechanical stimulus / peptide secretion / cellular response to temperature stimulus / excitatory extracellular ligand-gated monoatomic ion channel activity / temperature-gated ion channel activity / detection of chemical stimulus involved in sensory perception of pain / TRP channels / smooth muscle contraction involved in micturition ...negative regulation of establishment of blood-brain barrier / response to capsazepine / sensory perception of mechanical stimulus / peptide secretion / cellular response to temperature stimulus / excitatory extracellular ligand-gated monoatomic ion channel activity / temperature-gated ion channel activity / detection of chemical stimulus involved in sensory perception of pain / TRP channels / smooth muscle contraction involved in micturition / fever generation / urinary bladder smooth muscle contraction / thermoception / detection of temperature stimulus involved in thermoception / cellular response to acidic pH / negative regulation of systemic arterial blood pressure / response to pH / chloride channel regulator activity / dendritic spine membrane / glutamate secretion / monoatomic cation transmembrane transporter activity / cellular response to ATP / negative regulation of heart rate / ligand-gated monoatomic ion channel activity / response to pain / cellular response to alkaloid / temperature homeostasis / diet induced thermogenesis / cellular response to cytokine stimulus / detection of temperature stimulus involved in sensory perception of pain / intracellularly gated calcium channel activity / behavioral response to pain / negative regulation of mitochondrial membrane potential / calcium ion import across plasma membrane / monoatomic cation channel activity / extracellular ligand-gated monoatomic ion channel activity / sensory perception of pain / phosphatidylinositol binding / phosphoprotein binding / microglial cell activation / cellular response to nerve growth factor stimulus / GABA-ergic synapse / calcium ion transmembrane transport / calcium channel activity / cellular response to growth factor stimulus / response to peptide hormone / lipid metabolic process / positive regulation of nitric oxide biosynthetic process / calcium ion transport / transmembrane signaling receptor activity / cellular response to tumor necrosis factor / sensory perception of taste / cellular response to heat / positive regulation of cytosolic calcium ion concentration / response to heat / monoatomic ion transmembrane transport / protein homotetramerization / postsynaptic membrane / calmodulin binding / 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 / metal ion binding / identical protein binding / membrane / 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: 3.5 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: Structure of rat TRPV1 in complex with PSFL426-S5
Authors: Chen X / Yu Y
History
DepositionJul 17, 2024-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_60835.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)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density
Contour LevelBy AUTHOR: 0.095
Minimum - Maximum-0.27163053 - 0.3669278
Average (Standard dev.)0.0012360036 (±0.017598927)
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: #1

Fileemd_60835_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_60835_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : Structure of rat TRPV1 in complex with PSFL426-S5

EntireName: Structure of rat TRPV1 in complex with PSFL426-S5
Components
  • Complex: Structure of rat TRPV1 in complex with PSFL426-S5
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 1
  • Ligand: 4-azanyl-3-sulfanylidene-1,2,4-triazine-5,6-dione

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Supramolecule #1: Structure of rat TRPV1 in complex with PSFL426-S5

SupramoleculeName: Structure of rat TRPV1 in complex with PSFL426-S5 / 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: 99.645812 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKW SHPQFEKGGG GSGGSAWSHP QFEKEFKGLV DMEQRASLDS EESESPPQEN SCLDPPDRDP NCKPPPVKPH IFTTRSRTR LFGKGDSEEA SPLDCPYEEG GLASCPIITV SSVLTIQRPG DGPASVRPSS QDSVSAGEKP PRLYDRRSIF D AVAQSNCQ ...String:
MDYKDDDDKW SHPQFEKGGG GSGGSAWSHP QFEKEFKGLV DMEQRASLDS EESESPPQEN SCLDPPDRDP NCKPPPVKPH IFTTRSRTR LFGKGDSEEA SPLDCPYEEG GLASCPIITV SSVLTIQRPG DGPASVRPSS QDSVSAGEKP PRLYDRRSIF D AVAQSNCQ ELESLLPFLQ RSKKRLTDSE FKDPETGKTC LLKAMLNLHN GQNDTIALLL DVARKTDSLK QFVNASYTDS YY KGQTALH IAIERRNMTL VTLLVENGAD VQAAANGDFF KKTKGRPGFY FGELPLSLAA CTNQLAIVKF LLQNSWQPAD ISA RDSVGN TVLHALVEVA DNTVDNTKFV TSMYNEILIL GAKLHPTLKL EEITNRKGLT PLALAASSGK IGVLAYILQR EIHE PECRH LSRKFTEWAY GPVHSSLYDL SCIDTCEKNS VLEVIAYSSS ETPNRHDMLL VEPLNRLLQD KWDRFVKRIF YFNFF VYCL YMIIFTAAAY YRPVEGLPPY KLKNTVGDYF RVTGEILSVS GGVYFFFRGI QYFLQRRPSL KSLFVDSYSE ILFFVQ SLF MLVSVVLYFS QRKEYVASMV FSLAMGWTNM LYYTRGFQQM GIYAVMIEKM ILRDLCRFMF VYLVFLFGFS TAVVTLI ED GKNNSLPMES TPHKCRGSAC KPGNSYNSLY STCLELFKFT IGMGDLEFTE NYDFKAVFII LLLAYVILTY ILLLNMLI A LMGETVNKIA QESKNIWKLQ RAITILDTEK SFLKCMRKAF RSGKLLQVGF TPDGKDDYRW CFRVDEVNWT TWNTNVGII NEDPGNCEGV KRTLSFSLRS GRVSGRNWKN FALVPLLRDA STRDRHATQQ EEVQLKHYTG SLKPEDAEVF KDSMVPGEK

UniProtKB: Transient receptor potential cation channel subfamily V member 1

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Macromolecule #2: 4-azanyl-3-sulfanylidene-1,2,4-triazine-5,6-dione

MacromoleculeName: 4-azanyl-3-sulfanylidene-1,2,4-triazine-5,6-dione / type: ligand / ID: 2 / Number of copies: 4 / Formula: A1D92
Molecular weightTheoretical: 158.139 Da

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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
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: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15808
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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