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

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Basic information

Entry
Database: EMDB / ID: EMD-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.
Sample
  • Sample: Rat TRPV1
  • Protein or peptide: TRPV1
KeywordsTRPV1 channel
Function / homology
Function and homology information


response to capsazepine / negative regulation of establishment of blood-brain barrier / sensory perception of mechanical stimulus / excitatory extracellular ligand-gated monoatomic ion channel activity / peptide secretion / temperature-gated ion channel activity / detection of chemical stimulus involved in sensory perception of pain / cellular response to temperature stimulus / urinary bladder smooth muscle contraction / TRP channels ...response to capsazepine / negative regulation of establishment of blood-brain barrier / sensory perception of mechanical stimulus / excitatory extracellular ligand-gated monoatomic ion channel activity / peptide secretion / temperature-gated ion channel activity / detection of chemical stimulus involved in sensory perception of pain / cellular response to temperature stimulus / urinary bladder smooth muscle contraction / TRP channels / smooth muscle contraction involved in micturition / fever generation / thermoception / detection of temperature stimulus involved in thermoception / cellular response to acidic pH / response to pH / negative regulation of systemic arterial blood pressure / dendritic spine membrane / chloride channel regulator activity / monoatomic cation transmembrane transporter activity / glutamate secretion / negative regulation of heart rate / cellular response to ATP / response to pain / temperature homeostasis / cellular response to alkaloid / diet induced thermogenesis / cellular response to cytokine stimulus / intracellularly gated calcium channel activity / behavioral response to pain / detection of temperature stimulus involved in sensory perception of pain / negative regulation of mitochondrial membrane potential / calcium ion import across plasma membrane / ligand-gated monoatomic ion channel activity / monoatomic cation channel activity / extracellular ligand-gated monoatomic ion channel activity / sensory perception of pain / phosphatidylinositol binding / GABA-ergic synapse / phosphoprotein binding / microglial cell activation / cellular response to nerve growth factor stimulus / cellular response to growth factor stimulus / lipid metabolic process / calcium channel activity / calcium ion transmembrane transport / response to peptide hormone / calcium ion transport / transmembrane signaling receptor activity / positive regulation of nitric oxide biosynthetic process / sensory perception of taste / cellular response to tumor necrosis factor / cellular response to heat / response to heat / positive regulation of cytosolic calcium ion concentration / 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 / identical protein binding / membrane / metal ion binding / 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: 3.275 Å
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 /
Abstract: Transient receptor potential (TRP) channels are sensors for a wide range of cellular and environmental signals, but elucidating how these channels respond to physical and chemical stimuli has been ...Transient receptor potential (TRP) channels are sensors for a wide range of cellular and environmental signals, but elucidating how these channels respond to physical and chemical stimuli has been hampered by a lack of detailed structural information. Here we exploit advances in electron cryo-microscopy to determine the structure of a mammalian TRP channel, TRPV1, at 3.4 Å resolution, breaking the side-chain resolution barrier for membrane proteins without crystallization. Like voltage-gated channels, TRPV1 exhibits four-fold symmetry around a central ion pathway formed by transmembrane segments 5-6 (S5-S6) and the intervening pore loop, which is flanked by S1-S4 voltage-sensor-like domains. TRPV1 has a wide extracellular 'mouth' with a short selectivity filter. The conserved 'TRP domain' interacts with the S4-S5 linker, consistent with its contribution to allosteric modulation. Subunit organization is facilitated by interactions among cytoplasmic domains, including amino-terminal ankyrin repeats. These observations provide a structural blueprint for understanding unique aspects of TRP channel function.
History
DepositionOct 24, 2013-
Header (metadata) releaseDec 4, 2013-
Map releaseDec 4, 2013-
UpdateOct 14, 2015-
Current statusOct 14, 2015Processing 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-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 modelsPDB-3j9j
  • Imaged by Jmol
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5778_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5778.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure 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.
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)

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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-13.64936447 - 26.520059589999999
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
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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Supplemental map: emd 5778 additional 1.map

Fileemd_5778_additional_1.map
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Supplemental map: emd 5778 additional 2.map

Fileemd_5778_additional_2.map
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Supplemental map: emd 5778 additional 3.map

Fileemd_5778_additional_3.map
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Supplemental map: emd 5778 half map 1.map

Fileemd_5778_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Supplemental map: emd 5778 half map 2.map

Fileemd_5778_half_map_2.map
Projections & Slices
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Sample components

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Entire : Rat TRPV1

EntireName: Rat TRPV1
Components
  • Sample: Rat TRPV1
  • Protein or peptide: TRPV1

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Supramolecule #1000: Rat TRPV1

SupramoleculeName: Rat TRPV1 / 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 in super-resolution counting mode. Motion correction as described in Li et al. (2013) Nature Methods.
DateJan 1, 2013
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 946 / 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: 3.275 Å / Resolution method: OTHER / Software - Name: RELION / Number images used: 35645

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