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

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Entry
Database: EMDB / ID: 5777
TitleReconstruction of rat TRPV1 channel in complex with capsaicin by single particle cryo-microscopy
Map dataReconstruction of rat TRPV1 in complex with capsaicin
SampleRat TRPV1 in complex with capsaicin:
TRPV1
KeywordsTRPV1 channel / capsaicin
Function / homologyAnkyrin repeat-containing domain / Ion transport protein / Ankyrin repeat / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / TRP channels / Transient receptor potential channel / Ankyrin repeats (3 copies) / Transient receptor potential cation channel subfamily V / Ankyrin repeat-containing domain superfamily ...Ankyrin repeat-containing domain / Ion transport protein / Ankyrin repeat / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / TRP channels / Transient receptor potential channel / Ankyrin repeats (3 copies) / Transient receptor potential cation channel subfamily V / Ankyrin repeat-containing domain superfamily / Ion transport domain / Transient receptor potential channel, vanilloid 1-4 / Transient receptor potential cation channel subfamily V member 1 / response to capsazepine / peptide secretion / detection of temperature stimulus involved in thermoception / temperature-gated ion channel activity / sensory perception of mechanical stimulus / positive regulation of gastric acid secretion / thermoception / detection of chemical stimulus involved in sensory perception of pain / dendritic spine membrane / negative regulation of establishment of blood-brain barrier / smooth muscle contraction involved in micturition / excitatory extracellular ligand-gated ion channel activity / urinary bladder smooth muscle contraction / cellular response to temperature stimulus / diet induced thermogenesis / calcium ion import across plasma membrane / cellular response to acidic pH / fever generation / chloride channel regulator activity / temperature homeostasis / cation transmembrane transporter activity / behavioral response to pain / glutamate secretion / detection of temperature stimulus involved in sensory perception of pain / cation channel activity / calcium-release channel activity / intrinsic component of plasma membrane / response to pain / cellular response to ATP / cellular response to alkaloid / ligand-gated ion channel activity / extracellular ligand-gated ion channel activity / phosphatidylinositol binding / microglial cell activation / calcium channel activity / calcium ion transmembrane transport / cellular response to cytokine stimulus / sensory perception of pain / cellular response to nerve growth factor stimulus / response to organonitrogen compound / response to peptide hormone / calcium ion transport / lipid metabolic process / ion transmembrane transport / cellular response to growth factor stimulus / phosphoprotein binding / cellular response to heat / response to pH / transmembrane signaling receptor activity / cellular response to tumor necrosis factor / positive regulation of cytosolic calcium ion concentration / postsynaptic membrane / protein homotetramerization / response to heat / positive regulation of nitric oxide biosynthetic process / ion channel activity / calmodulin binding / neuron projection / synapse / cell junction / dendrite / neuronal cell body / external side of plasma membrane / inflammatory response / positive regulation of apoptotic process / integral component of plasma membrane / negative regulation of transcription by RNA polymerase II / membrane / integral component of membrane / ATP binding / identical protein binding / plasma membrane / metal ion binding / cytosol / Transient receptor potential cation channel subfamily V member 1
Function and homology information
SourceRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / 4.2 Å resolution
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.
Validation ReportPDB-ID: 3j5r

SummaryFull reportAbout validation report
DateDeposition: Oct 24, 2013 / Header (metadata) release: Dec 4, 2013 / Map release: Dec 4, 2013 / Last update: Dec 18, 2013

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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:
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Supplemental images

Downloads & links

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Map

Fileemd_5777.map.gz (map file in CCP4 format, 65537 KB)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.22 Å/pix.
= 311.194 Å
256 pix
1.22 Å/pix.
= 311.194 Å
256 pix
1.22 Å/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
Contour Level:7 (by author), 7 (movie #1):
Minimum - Maximum-8.71960831 - 22.64736557
Average (Standard dev.)0E-8 (1)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin-128-128-128
Limit127127127
Spacing256256256
CellA=B=C: 311.1936 Å
α=β=γ: 90 deg.

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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Sample components

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Entire Rat TRPV1 in complex with capsaicin

EntireName: Rat TRPV1 in complex with capsaicin / Details: The sample was monodisperse. / Number of components: 1 / Oligomeric State: tetramer
MassTheoretical: 300 kDa / Experimental: 300 kDa

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Component #1: protein, TRPV1

ProteinName: TRPV1 / Oligomeric Details: Tetramer
Details: Functional minimal construct containing residues 110-603 and 627-764.
Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 300 kDa / Experimental: 300 kDa
SourceSpecies: Rattus norvegicus (Norway rat)
Source (engineered)Expression System: Homo sapiens (human) / Vector: pFastBac1 / Cell of expression system: HEK293S GnTI
Source (natural)Location in cell: Plasma membrane
External referencesUniProt: UniProt:O35433

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.3 mg/ml / Buffer solution: 150 mM NaCl, 20 mM HEPES, 2 mM TCEP / pH: 7.4
Support film400 mesh Quantifoil grid
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 120 K / Humidity: 90 % / Method: Blot for 6 sec

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300 / Date: Jan 1, 2013
Details: Gatan K2 Summit operated in super-resolution counting mode; image recorded with dose fractionation method.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 21 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 31000 X (nominal), 31000 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 3000 nm
Specimen HolderHolder: Cooled to Liquid Nitrogen temperature / Model: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 900
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.

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C4 (4 fold cyclic) / Number of projections: 33238
Details: 3D classification, refinement, and reconstruction were performed using RELION.
3D reconstructionAlgorithm: Maximum likelihood / Software: RELION / CTF correction: Each particle / Resolution: 4.2 Å / Resolution method: Gold standard FSC at 0.143 cut-off

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Atomic model buiding

Output model

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