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- EMDB-5777: Reconstruction of rat TRPV1 channel in complex with capsaicin by ... -

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Basic information

Entry
Database: EMDB / ID: EMD-5777
TitleReconstruction of rat TRPV1 channel in complex with capsaicin by single particle cryo-microscopy
Map dataReconstruction of rat TRPV1 in complex with capsaicin
Sample
  • Sample: Rat TRPV1 in complex with capsaicin
  • Protein or peptide: TRPV1
KeywordsTRPV1 channel / capsaicin
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 / detection of temperature stimulus involved in thermoception / thermoception / cellular response to acidic pH / negative regulation of systemic arterial blood pressure / chloride channel regulator activity / response to pH / 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 / calcium ion transmembrane transport / GABA-ergic synapse / 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 / neuron projection / calmodulin binding / 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: 4.2 Å
AuthorsLiao M / Cao E / Julius D / Cheng Y
CitationJournal: Nature / Year: 2013
Title: TRPV1 structures in distinct conformations reveal activation mechanisms.
Authors: Erhu Cao / Maofu Liao / Yifan Cheng / David Julius /
Abstract: Transient receptor potential (TRP) channels are polymodal signal detectors that respond to a wide range of physical and chemical stimuli. Elucidating how these channels integrate and convert ...Transient receptor potential (TRP) channels are polymodal signal detectors that respond to a wide range of physical and chemical stimuli. Elucidating how these channels integrate and convert physiological signals into channel opening is essential to understanding how they regulate cell excitability under normal and pathophysiological conditions. Here we exploit pharmacological probes (a peptide toxin and small vanilloid agonists) to determine structures of two activated states of the capsaicin receptor, TRPV1. A domain (consisting of transmembrane segments 1-4) that moves during activation of voltage-gated channels remains stationary in TRPV1, highlighting differences in gating mechanisms for these structurally related channel superfamilies. TRPV1 opening is associated with major structural rearrangements in the outer pore, including the pore helix and selectivity filter, as well as pronounced dilation of a hydrophobic constriction at the lower gate, suggesting a dual gating mechanism. Allosteric coupling between upper and lower gates may account for rich physiological modulation exhibited by TRPV1 and other TRP channels.
History
DepositionOct 24, 2013-
Header (metadata) releaseDec 4, 2013-
Map releaseDec 4, 2013-
UpdateDec 18, 2013-
Current statusDec 18, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 7
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 7
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j5r
  • Surface level: 7
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5777_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5777.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of rat TRPV1 in complex with capsaicin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.22 Å/pix.
x 256 pix.
= 311.194 Å		1.22 Å/pix.
x 256 pix.
= 311.194 Å		1.22 Å/pix.
x 256 pix.
= 311.194 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2156 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.0 / Movie #1: 7
Minimum - Maximum-8.71960831 - 22.647365570000002
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 311.1936 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.21560156251.21560156251.2156015625
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z311.194311.194311.194
α/β/γ90.00090.00090.000
start NX/NY/NZ-95-75153
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-8.72022.6470.000

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Supplemental data

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Supplemental map: emd 5777 additional 1.map

Fileemd_5777_additional_1.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 : Rat TRPV1 in complex with capsaicin

EntireName: Rat TRPV1 in complex with capsaicin
Components
  • Sample: Rat TRPV1 in complex with capsaicin
  • Protein or peptide: TRPV1

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Supramolecule #1000: Rat TRPV1 in complex with capsaicin

SupramoleculeName: Rat TRPV1 in complex with capsaicin / type: sample / ID: 1000 / Details: The sample was monodisperse. / Oligomeric state: tetramer / Number unique components: 1
Molecular weightExperimental: 300 KDa / Theoretical: 300 KDa

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Macromolecule #1: TRPV1

MacromoleculeName: TRPV1 / type: protein_or_peptide / ID: 1
Details: Functional minimal construct containing residues 110-603 and 627-764.
Number of copies: 1 / Oligomeric state: Tetramer / Recombinant expression: Yes
Source (natural)Organism: Rattus norvegicus (Norway rat) / synonym: Rat / Location in cell: Plasma membrane
Molecular weightExperimental: 300 KDa / Theoretical: 300 KDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293S GnTI / Recombinant plasmid: pFastBac1
SequenceUniProtKB: Transient receptor potential cation channel subfamily V member 1

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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

Concentration0.3 mg/mL
BufferpH: 7.4 / Details: 150 mM NaCl, 20 mM HEPES, 2 mM TCEP
GridDetails: 400 mesh Quantifoil grid
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK III / Method: Blot for 6 sec

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Electron microscopy

MicroscopeFEI POLARA 300
DetailsGatan K2 Summit operated in super-resolution counting mode; image recorded with dose fractionation method.
DateJan 1, 2013
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 900 / Average electron dose: 21 e/Å2
Details: Every image is the average of 30 frames recorded using the K2 Summit. The final reconstruction was calculated from images averaged from frames #3-#16.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 31000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 31000
Sample stageSpecimen holder: Cooled to Liquid Nitrogen temperature / Specimen holder model: OTHER
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Details3D classification, refinement, and reconstruction were performed using RELION.
CTF correctionDetails: Each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: OTHER / Software - Name: RELION / Number images used: 33238

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