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- EMDB-8117: Structure of TRPV1 in complex with DkTx and RTX, determined in li... -

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Basic information

Entry
Database: EMDB / ID: 8117
TitleStructure of TRPV1 in complex with DkTx and RTX, determined in lipid nanodisc
Map dataTRPV1 in complex with DkTx and RTX
SampleTRPV1 ion channel in complex with DkTx and RTX
  • (Transient receptor potential cation channel subfamily V member ...) x 2
  • (Tau-theraphotoxin- ...) x 2
  • (ligand) x 4
Function / homologyTransient receptor potential channel, vanilloid 1-4 / Transient receptor potential cation channel subfamily V / Transient receptor potential cation channel subfamily V member 1 / Ion transport domain / Ankyrin repeat / Ankyrin repeat-containing domain / Ankyrin repeat-containing domain superfamily / Ion transport protein / TRP channels / Ankyrin repeat region circular profile. ...Transient receptor potential channel, vanilloid 1-4 / Transient receptor potential cation channel subfamily V / Transient receptor potential cation channel subfamily V member 1 / Ion transport domain / Ankyrin repeat / Ankyrin repeat-containing domain / Ankyrin repeat-containing domain superfamily / Ion transport protein / TRP channels / Ankyrin repeat region circular profile. / Ankyrin repeat profile. / Ankyrin repeats (3 copies) / 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 / smooth muscle contraction involved in micturition / detection of chemical stimulus involved in sensory perception of pain / 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 / behavioral response to pain / cellular response to temperature stimulus / fever generation / calcium ion import across plasma membrane / 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 alkaloid / cellular response to ATP / extracellular ligand-gated ion channel activity / phosphatidylinositol binding / calcium channel activity / microglial cell activation / cellular response to cytokine stimulus / calcium ion transmembrane transport / calcium ion transport / cellular response to growth factor stimulus / cellular response to nerve growth factor stimulus / response to peptide hormone / lipid metabolic process / phosphoprotein binding / response to pH / postsynaptic membrane / cellular response to heat / cellular response to tumor necrosis factor / positive regulation of cytosolic calcium ion concentration / protein homotetramerization / ion channel activity / positive regulation of nitric oxide biosynthetic process / response to heat / transmembrane signaling receptor activity / toxin activity / calmodulin binding / lipid 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 / membrane / integral component of membrane / extracellular region / ATP binding / identical protein binding / plasma membrane / metal ion binding / cytosol / Transient receptor potential cation channel subfamily V member 1 / Tau-theraphotoxin-Hs1a
Function and homology information
SourceRattus norvegicus (Norway rat) / Haplopelma schmidti (Chinese earth tiger)
Methodsingle particle reconstruction / cryo EM / 2.95 Å resolution
AuthorsGao Y / Cao E / Julius D / Cheng Y
CitationJournal: Nature / Year: 2016
Title: TRPV1 structures in nanodiscs reveal mechanisms of ligand and lipid action.
Authors: Yuan Gao / Erhu Cao / David Julius / Yifan Cheng
Validation ReportPDB-ID: 5irx

SummaryFull reportAbout validation report
DateDeposition: May 16, 2016 / Header (metadata) release: May 25, 2016 / Map release: May 25, 2016 / Last update: Sep 13, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5irx
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8117.map.gz (map file in CCP4 format, 28312 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
192 pix
1.22 Å/pix.
= 233.395 Å
192 pix
1.22 Å/pix.
= 233.395 Å
192 pix
1.22 Å/pix.
= 233.395 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:3.5 (by emdb), 4 (movie #1):
Minimum - Maximum-14.310627999999999 - 24.292179999999998
Average (Standard dev.)-0.000000004099751 (0.99999994)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions192192192
Origin0.00.00.0
Limit191.0191.0191.0
Spacing192192192
CellA=B=C: 233.3952 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.21559895833331.21559895833331.2155989583333
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z233.395233.395233.395
α/β/γ90.00090.00090.000
start NX/NY/NZ-25-77-48
NX/NY/NZ899896
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-14.31124.292-0.000

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Supplemental data

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Sample components

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Entire TRPV1 ion channel in complex with DkTx and RTX

EntireName: TRPV1 ion channel in complex with DkTx and RTX
Details: Two molecules of DkTx and 4 molecules of RTX bound to one TRPV1 homo-tetramer
Number of components: 9

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Component #1: protein, TRPV1 ion channel in complex with DkTx and RTX

ProteinName: TRPV1 ion channel in complex with DkTx and RTX
Details: Two molecules of DkTx and 4 molecules of RTX bound to one TRPV1 homo-tetramer
Recombinant expression: No

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Component #2: protein, Transient receptor potential cation channel subfamily V ...

ProteinName: Transient receptor potential cation channel subfamily V member 1
Recombinant expression: No
SourceSpecies: Rattus norvegicus (Norway rat)
Source (engineered)Expression System: Homo sapiens (human) / Vector: unknown

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Component #3: protein, Tau-theraphotoxin-Hs1a

ProteinName: Tau-theraphotoxin-Hs1a / Recombinant expression: No
SourceSpecies: Haplopelma schmidti (Chinese earth tiger)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria) / Vector: unknown

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Component #4: protein, Transient receptor potential cation channel subfamily V ...

ProteinName: Transient receptor potential cation channel subfamily V member 1
Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 72.959297 kDa
SourceSpecies: Rattus norvegicus (Norway rat)
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, Tau-theraphotoxin-Hs1a

ProteinName: Tau-theraphotoxin-Hs1a / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 8.552988 kDa
SourceSpecies: Haplopelma schmidti (Chinese earth tiger)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #6: ligand, (4R,7S)-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-7-[(pentanoyl...

LigandName: (4R,7S)-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-7-[(pentanoyloxy)methyl]-3,5,8-trioxa-4lambda~5~-phosphatetradecan-1-aminium
Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.440489 kDa

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Component #7: ligand, (2S)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(h...

LigandName: (2S)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexanoyloxy)propyl hexanoate
Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 0.411428 kDa

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Component #8: ligand, resiniferatoxin

LigandName: resiniferatoxin / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.628708 kDa

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Component #9: ligand, (2S)-2-(acetyloxy)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosph...

LigandName: (2S)-2-(acetyloxy)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}propyl pentanoate
Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.341295 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.5 mg/ml / pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 278 K / Humidity: 100 %
Details: Blot for 6 seconds before plunging into liquid ethane (FEI VITROBOT MARK III)..

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300 / Details: Grid screening was performed manually.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 41 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 31000.0 X (nominal), 41132.0 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 700.0 - 2200.0 nm
Specimen HolderModel: OTHER / Temperature: K ( 70.0 - 70.0 K)
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1200
Details: Images were collected in movie mode at 5 frames per second for 6 seconds.
Raw dataEMPIAR-10059 (Title: Structure of TRPV1 in complex with DkTx and RTX, determined in lipid nanodisc
Data size: 93.8
Data #1: Motion corrected, dose-weighted sum of micrographs of TRPV1-DkTx/RTX embedded in lipid nanodisc [micrographs - single frame]
Data #2: Raw particle image stack of TRPV1-DkTx/RTX embedded in lipid nanodisc [picked particles - multiframe - unprocessed])

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C4 (4 fold cyclic) / Number of projections: 73929
Details: Each image stack was subjected to whole-frame motion correction followed by correction at the individual pixel level using program UcsfDfCorr.
3D reconstructionSoftware: RELION
CTF correction: CTF correction was performed before classification and refinement.
Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Target criteria: correlation coefficient / Refinement space: REAL
Input PDB model: 3J5Q
Chain ID: A
Output model

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