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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
SampleTRPV1 ion channel in complex with DkTx and RTX
SourceRattus norvegicus / mammal / ドブネズミ, どぶねずみ /
Haplopelma schmidti / arthropod / spider
Map dataTRPV1 in complex with DkTx and RTX
Methodsingle particle reconstruction, at 2.95 A resolution
AuthorsGao Y / Cao E
CitationNature, 2016, 534, 347-351

Nature, 2016, 534, 347-351 StrPapers
TRPV1 structures in nanodiscs reveal mechanisms of ligand and lipid action.
Yuan Gao / Erhu Cao / David Julius / Yifan Cheng

DateDeposition: May 16, 2016 / Header (metadata) release: May 25, 2016 / Map release: May 25, 2016 / Last update: May 16, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF CHIMERA
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  • Surface view colored by cylindrical radius
  • Surface level: 4
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5irx
  • Surface level: 4
  • Imaged by UCSF CHIMERA
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Supplemental images

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Map

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

Image control

Size
Brightness
Contrast
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AxesZ (Sec.)Y (Row.)X (Col.)
192 pix
1.22 A/pix
= 233.395 A
192 pix
1.22 A/pix
= 233.395 A
192 pix
1.22 A/pix
= 233.395 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.2156 A
Density
Contour Level:3.5 (by emdb), 4 (movie #1):
Minimum - Maximum-14.310628 - 24.29218
Average (Standard dev.)-4.099751E-9 (0.99999994)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions192192192
Origin000
Limit191191191
Spacing192192192
CellA=B=C: 233.3952 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
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 / mammal / ドブネズミ, どぶねずみ /
Source (engineered)Expression System: Homo sapiens / human

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Component #3: protein, Tau-theraphotoxin-Hs1a

ProteinName: Tau-theraphotoxin-Hs1a / Recombinant expression: No
SourceSpecies: Haplopelma schmidti / arthropod / spider
Source (engineered)Expression System: Escherichia coli bl21(de3) / bacteria / image: Escherichia coli

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

ProteinName: Transient receptor potential cation channel subfamily V member 1
Recombinant expression: No
MassTheoretical: 72.959297 kDa
Source (engineered)Expression System: Rattus norvegicus / mammal / ドブネズミ, どぶねずみ /

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Component #5: protein, Tau-theraphotoxin-Hs1a

ProteinName: Tau-theraphotoxin-Hs1a / Recombinant expression: No
MassTheoretical: 8.552988 kDa
Source (engineered)Expression System: Haplopelma schmidti / arthropod / spider / Vector: pET19

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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

Specimen stateparticle
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

ImagingMicroscope: FEI POLARA 300 / Details: Grid screening was performed manually.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 41 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 31000 X (nominal), 41132 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 700 - 2200 nm
Specimen HolderModel: OTHER / Temperature: K ( 70 - 70 K)
CameraDetector: GATAN K2 (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 (Name: Motion corrected, dose-weighted sum of micrographs of TRPV1-DkTx/RTX embedded in lipid nanodisc
Category: micrographs - single frame / Data size: 93.8 GB)

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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 A / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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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: 3J5Q_A
Output model

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