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- EMDB-5778: Structure of the capsaicin receptor, TRPV1, determined by single ... -

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Entry
Database: EMDB / ID: 5778
TitleStructure of the capsaicin receptor, TRPV1, determined by single particle electron cryo-microscopy
Map dataStructure of the capsaicin receptor, TRPV1. This map is direct output from RELION without sharpening using a negative temperature factor. The map was normalized using the program MAPMAN.
SampleRat TRPV1:
TRPV1
KeywordsTRPV1 channel
Function / homologyTransient receptor potential channel, vanilloid 1-4 / TRP channels / Ion transport domain / Ankyrin repeat-containing domain / Transient receptor potential cation channel subfamily V / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat-containing domain superfamily / Transient receptor potential cation channel subfamily V member 1 / Ion transport protein ...Transient receptor potential channel, vanilloid 1-4 / TRP channels / Ion transport domain / Ankyrin repeat-containing domain / Transient receptor potential cation channel subfamily V / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat-containing domain superfamily / Transient receptor potential cation channel subfamily V member 1 / Ion transport protein / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / detection of temperature stimulus involved in thermoception / excitatory extracellular ligand-gated ion channel activity / response to capsazepine / temperature-gated ion channel activity / peptide secretion / sensory perception of mechanical stimulus / smooth muscle contraction involved in micturition / positive regulation of gastric acid secretion / detection of chemical stimulus involved in sensory perception of pain / dendritic spine membrane / negative regulation of establishment of blood-brain barrier / diet induced thermogenesis / ligand-gated ion channel activity / cellular response to acidic pH / negative regulation of systemic arterial blood pressure / cellular response to temperature stimulus / fever generation / behavioral response to pain / calcium ion import across plasma membrane / chloride channel regulator activity / glutamate secretion / cation transmembrane transporter activity / negative regulation of mitochondrial membrane potential / negative regulation of heart rate / detection of temperature stimulus involved in sensory perception of pain / cation channel activity / calcium-release channel activity / intrinsic component of plasma membrane / cellular response to alkaloid / cellular response to ATP / extracellular ligand-gated ion channel activity / phosphatidylinositol binding / calcium channel activity / microglial cell activation / calcium ion transmembrane transport / cellular response to cytokine stimulus / calcium ion transport / cellular response to growth factor stimulus / response to peptide hormone / cellular response to nerve growth factor stimulus / lipid metabolic process / phosphoprotein binding / response to pH / postsynaptic membrane / transmembrane signaling receptor activity / cellular response to tumor necrosis factor / positive regulation of cytosolic calcium ion concentration / protein homotetramerization / cellular response to heat / positive regulation of nitric oxide biosynthetic process / ion channel activity / response to heat / calmodulin binding / cell junction / synapse / inflammatory response / external side of plasma membrane / positive regulation of apoptotic process / dendrite / neuronal cell body / integral component of plasma membrane / negative regulation of transcription by RNA polymerase II / mitochondrion / 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 / 3.275 Å resolution
AuthorsLiao M / Cao E / Julius D / Cheng Y
CitationJournal: Nature / Year: 2013
Title: Structure of the TRPV1 ion channel determined by electron cryo-microscopy.
Authors: Maofu Liao / Erhu Cao / David Julius / Yifan Cheng
Validation ReportPDB-ID: 3j5p

SummaryFull report
PDB-ID: 3j9j

SummaryFull report
About validation report
DateDeposition: Oct 24, 2013 / Header (metadata) release: Dec 4, 2013 / Map release: Dec 4, 2013 / Last update: Oct 14, 2015

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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-3j5p
  • Surface level: 7
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-3j9j
  • Surface level: 7
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-3j9j
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_5778.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-13.64936447 - 26.52005959
Average (Standard dev.)0E-8 (1.00000000)
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: 90.0 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
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-13.64926.520-0.000

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Supplemental data

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Sample components

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Entire Rat TRPV1

EntireName: Rat TRPV1 / 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 in super-resolution counting mode. Motion correction as described in Li et al. (2013) Nature Methods.
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: 946
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.
URL of raw data: http://dx.doi.org/10.6019/EMPIAR-10005
Raw dataEMPIAR-10005 (Title: TRPV1 dataset taken on a K2 direct electron detector / Data size: 6.3 TB / Data #1: TRPV1 picked particles [tilt series]
Data #2: TRPV1 raw multi-frame micrographs [micrographs - multiframe]
Data #3: TRPV1 summed frame micrographs [micrographs - single frame])

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C4 (4 fold cyclic) / Number of projections: 35645
Details: 3D classification, refinement, and reconstruction were performed using RELION.
3D reconstructionAlgorithm: Maximum likelihood / Software: RELION / CTF correction: Each particle / Resolution: 3.275 Å / Resolution method: Gold standard FSC at 0.143 cut-off

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