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- EMDB-7121: Cryo-EM structure of human TRPV6 in amphipols -

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Basic information

Entry
Database: EMDB / ID: 7121
TitleCryo-EM structure of human TRPV6 in amphipols
Map dataprimary map
SampleTRPV6 ion channel in open states
  • Transient receptor potential cation channel subfamily V member 6
Function/homologyTransient receptor potential channel, vanilloid 6 / Transient receptor potential cation channel subfamily V member 5/6 / calcium ion import across plasma membrane / TRP channels / Transient receptor potential cation channel subfamily V / Transient receptor potential channel / regulation of calcium ion-dependent exocytosis / calcium ion homeostasis / Ankyrin repeat / calcium channel activity ...Transient receptor potential channel, vanilloid 6 / Transient receptor potential cation channel subfamily V member 5/6 / calcium ion import across plasma membrane / TRP channels / Transient receptor potential cation channel subfamily V / Transient receptor potential channel / regulation of calcium ion-dependent exocytosis / calcium ion homeostasis / Ankyrin repeat / calcium channel activity / calcium ion transmembrane transport / Ion transport domain / calcium ion transport / Ion transport protein / Ankyrin repeat profile. / Ankyrin repeat / Ankyrin repeat region circular profile. / Ankyrin repeat-containing domain / Ankyrin repeat-containing domain superfamily / response to calcium ion / Ankyrin repeats (3 copies) / calmodulin binding / integral component of plasma membrane / extracellular exosome / plasma membrane / metal ion binding / Transient receptor potential cation channel subfamily V member 6
Function and homology information
SourceHomo sapiens / / human
MethodCryo EM / single particle reconstruction / 4 Å resolution
AuthorsMcGoldrick LL / Singh AK
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
Abstract: Calcium-selective transient receptor potential vanilloid subfamily member 6 (TRPV6) channels play a critical role in calcium uptake in epithelial tissues. Altered TRPV6 expression is associated with ...Calcium-selective transient receptor potential vanilloid subfamily member 6 (TRPV6) channels play a critical role in calcium uptake in epithelial tissues. Altered TRPV6 expression is associated with a variety of human diseases, including cancers. TRPV6 channels are constitutively active and their open probability depends on the lipidic composition of the membrane in which they reside; it increases substantially in the presence of phosphatidylinositol 4,5-bisphosphate. Crystal structures of detergent-solubilized rat TRPV6 in the closed state have previously been solved. Corroborating electrophysiological results, these structures demonstrated that the Ca selectivity of TRPV6 arises from a ring of aspartate side chains in the selectivity filter that binds Ca tightly. However, how TRPV6 channels open and close their pores for ion permeation has remained unclear. Here we present cryo-electron microscopy structures of human TRPV6 in the open and closed states. The channel selectivity filter adopts similar conformations in both states, consistent with its explicit role in ion permeation. The iris-like channel opening is accompanied by an α-to-π-helical transition in the pore-lining transmembrane helix S6 at an alanine hinge just below the selectivity filter. As a result of this transition, the S6 helices bend and rotate, exposing different residues to the ion channel pore in the open and closed states. This gating mechanism, which defines the constitutive activity of TRPV6, is, to our knowledge, unique among tetrameric ion channels and provides structural insights for understanding their diverse roles in physiology and disease.
Validation ReportPDB-ID: 6bo9

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: 0.0388
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0388
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-6bo9
  • Surface level: 0.0388
  • Imaged by UCSF CHIMERA
  • Download
3D viewer
Supplemental images

Downloads & links

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Map

Fileemd_7121.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 package.

Voxel sizeX=Y=Z: 0.98 Å
Density
Contour Level:0.0388 (by author), 0.0388 (movie #1):
Minimum - Maximum-0.10382786 - 0.17157836
Average (Standard dev.)0.0011041488 (0.00793931)
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-0.1040.1720.001

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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.: 0.3 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: 65259
3D reconstructionSoftware: RELION / Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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