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- EMDB-5776: Structure of the capsaicin receptor, TRPV1, in complex with DkTx ... -

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Basic information

Entry
Database: EMDB / ID: 5776
TitleStructure of the capsaicin receptor, TRPV1, in complex with DkTx and RTX determined by single particle electron cryo-microscopy
Map dataReconstruction of rat TRPV1 channel in complex with DkTx and RTX
SampleRat TRPV1 in complex with DkTx and resiniferatoxin:
TRPV1
KeywordsTRPV1 channel / DkTx / RTX
Function / homologyAnkyrin repeat-containing domain / Ankyrin repeat profile. / Transient receptor potential channel, vanilloid 1-4 / Ion transport domain / in:ipr004729: / Ankyrin repeat / Transient receptor potential cation channel subfamily V member 1 / Transient receptor potential cation channel subfamily V / Ion transport protein / Ankyrin repeats (3 copies) ...Ankyrin repeat-containing domain / Ankyrin repeat profile. / Transient receptor potential channel, vanilloid 1-4 / Ion transport domain / in:ipr004729: / Ankyrin repeat / Transient receptor potential cation channel subfamily V member 1 / Transient receptor potential cation channel subfamily V / Ion transport protein / Ankyrin repeats (3 copies) / Ankyrin repeat-containing domain superfamily / Ankyrin repeat region circular profile. / TRP channels / detection of temperature stimulus involved in thermoception / peptide secretion / temperature-gated ion channel activity / response to capsazepine / sensory perception of mechanical stimulus / positive regulation of gastric acid secretion / detection of chemical stimulus involved in sensory perception of pain / smooth muscle contraction involved in micturition / dendritic spine membrane / negative regulation of establishment of blood-brain barrier / excitatory extracellular ligand-gated ion channel activity / diet induced thermogenesis / cellular response to acidic pH / cellular response to temperature stimulus / behavioral response to pain / calcium ion import across plasma membrane / fever generation / chloride channel regulator activity / cation transmembrane transporter activity / glutamate secretion / cation channel activity / detection of temperature stimulus involved in sensory perception of pain / ligand-gated ion channel activity / calcium-release channel activity / intrinsic component of plasma membrane / cellular response to ATP / cellular response to alkaloid / extracellular ligand-gated ion channel activity / phosphatidylinositol binding / microglial cell activation / calcium ion transmembrane transport / cellular response to cytokine stimulus / cellular response to growth factor stimulus / cellular response to nerve growth factor stimulus / calcium ion transport / response to peptide hormone / lipid metabolic process / cellular response to heat / phosphoprotein binding / 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 / calmodulin binding / synapse / cell junction / external side of plasma membrane / inflammatory response / positive regulation of apoptotic process / dendrite / neuronal cell body / 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 / 3.8 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
Validation ReportPDB-ID: 3j5q

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
  • Download
  • 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-3j5q
  • Surface level: 7
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_5776.map.gz (map file in CCP4 format, 65537 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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-11.82768822 - 22.92388535
Average (Standard dev.)0E-8 (1.00000012)
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-11.82822.924-0.000

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Supplemental data

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Sample components

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Entire Rat TRPV1 in complex with DkTx and resiniferatoxin

EntireName: Rat TRPV1 in complex with DkTx and resiniferatoxin / 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: Transient receptor potential cation channel subfamily V member 1

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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: 36158
Details: 3D classification, refinement, and reconstruction were performed using RELION.
3D reconstructionAlgorithm: Maximum likelihood / Software: RELION / CTF correction: Each particle / Resolution: 3.8 Å / Resolution method: Gold standard FSC at 0.143 cut-off

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Atomic model buiding

Output model

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