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- EMDB-7120: Cryo-EM structure of human TRPV6 in nanodiscs -

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Open data


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Basic information

Entry
Database: EMDB / ID: 7120
TitleCryo-EM structure of human TRPV6 in nanodiscs
Map dataprimary map
SampleTRPV6 ion channel in open states
  • Transient receptor potential cation channel subfamily V member 6
Function / homologyIon transport domain / Ankyrin repeat / Transient receptor potential channel, vanilloid 6 / Transient receptor potential cation channel subfamily V member 5/6 / Ankyrin repeat-containing domain superfamily / Transient receptor potential channel / Ankyrin repeat / Ankyrin repeat-containing domain / Transient receptor potential cation channel subfamily V / Ion transport protein ...Ion transport domain / Ankyrin repeat / Transient receptor potential channel, vanilloid 6 / Transient receptor potential cation channel subfamily V member 5/6 / Ankyrin repeat-containing domain superfamily / Transient receptor potential channel / Ankyrin repeat / Ankyrin repeat-containing domain / Transient receptor potential cation channel subfamily V / Ion transport protein / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / TRP channels / calcium ion import across plasma membrane / regulation of calcium ion-dependent exocytosis / calcium ion homeostasis / calcium channel activity / calcium ion transmembrane transport / calcium ion transport / response to calcium ion / calmodulin binding / integral component of plasma membrane / plasma membrane / metal ion binding / Transient receptor potential cation channel subfamily V member 6
Function and homology information
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 3.6 Å resolution
AuthorsMcGoldrick LL / Singh AK / Saotome K / Yelshanskaya MV / Twomey EC / Grassucci RA / Sobolevsky AI
CitationJournal: Nature / Year: 2018
Title: Opening of the human epithelial calcium channel TRPV6.
Authors: Luke L McGoldrick / Appu K Singh / Kei Saotome / Maria V Yelshanskaya / Edward C Twomey / Robert A Grassucci / Alexander I Sobolevsky
Validation ReportPDB-ID: 6bo8

SummaryFull reportAbout validation report
DateDeposition: Nov 18, 2017 / Header (metadata) release: Dec 6, 2017 / Map release: Dec 20, 2017 / Last update: Jan 24, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0469
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0469
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6bo8
  • Surface level: 0.0469
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7120.map.gz (map file in CCP4 format, 33959 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
204 pix
0.98 Å/pix.
= 199.92 Å
204 pix
0.98 Å/pix.
= 199.92 Å
204 pix
0.98 Å/pix.
= 199.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.98 Å
Density
Contour Level:0.0469 (by author), 0.0469 (movie #1):
Minimum - Maximum-0.13082665 - 0.23039147
Average (Standard dev.)0.0010486454 (0.0099845305)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions204204204
Origin000
Limit203203203
Spacing204204204
CellA=B=C: 199.92 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.980.980.98
M x/y/z204204204
origin x/y/z0.0000.0000.000
length x/y/z199.920199.920199.920
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS204204204
D min/max/mean-0.1310.2300.001

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Supplemental data

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Sample components

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Entire TRPV6 ion channel in open states

EntireName: TRPV6 ion channel in open states / Number of components: 2

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Component #1: protein, TRPV6 ion channel in open states

ProteinName: TRPV6 ion channel in open states / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: HEK-293 cells

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

ProteinName: Transient receptor potential cation channel subfamily V member 6
Recombinant expression: No
MassTheoretical: 85.168953 kDa
Source (engineered)Expression System: Homo sapiens (human)

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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 / Buffer solution: TRIS, NaCl, / pH: 8
VitrificationCryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 67 e/Å2 / Illumination mode: SPOT SCAN
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 46124
3D reconstructionSoftware: RELION / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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