[English] 日本語
Yorodumi
- PDB-6boa: Cryo-EM structure of human TRPV6-R470E in amphipols -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6boa
TitleCryo-EM structure of human TRPV6-R470E in amphipols
ComponentsTransient receptor potential cation channel subfamily V member 6
KeywordsTRANSPORT PROTEIN / Ion channel / Membrane protein
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
Specimen sourceHomo sapiens / / human
MethodElectron microscopy (4.2 Å resolution / Particle / Single particle) / Transmission electron microscopy
AuthorsMcGoldrick, L.L. / Singh, A.K. / Saotome, K. / Yelshanskaya, M.V. / Twomey, E.C. / Grassucci, R.A. / Sobolevsky, A.I.
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 Report
SummaryFull reportAbout validation report
DateDeposition: Nov 18, 2017 / Release: Dec 20, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 20, 2017Structure modelrepositoryInitial release
1.1Jan 3, 2018Structure modelDatabase referencescitation_citation.pdbx_database_id_PubMed / _citation.title
1.2Jan 17, 2018Structure modelAuthor supporting evidencepdbx_audit_support_pdbx_audit_support.funding_organization
1.3Jan 24, 2018Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
3D viewer

Downloads & links

-
Assembly

Deposited unit
A: Transient receptor potential cation channel subfamily V member 6
B: Transient receptor potential cation channel subfamily V member 6
C: Transient receptor potential cation channel subfamily V member 6
D: Transient receptor potential cation channel subfamily V member 6


Theoretical massNumber of molelcules
Total (without water)340,5644
Polyers340,5644
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein/peptide
Transient receptor potential cation channel subfamily V member 6 / TrpV6 / CaT-like / CaT-L / Calcium transport protein 1 / CaT1 / Epithelial calcium channel 2 / ECaC2


Mass: 85140.875 Da / Num. of mol.: 4 / Mutation: R470E / Source: (gene. exp.) Homo sapiens / / human / Gene: TRPV6, ECAC2 / Production host: Homo sapiens / References: UniProt:Q9H1D0

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

-
Sample preparation

ComponentName: TRPV6-R470E ion channel in closed states / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens
Source (recombinant)Organism: HEK-293 cells
Buffer solutionDetails: TRIS, NaCl, / pH: 8
Buffer component
IDConc.FormulaBuffer ID
150TRIS1
2150NaCl1
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: C-flat-1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 67 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM softwareName: RELION / Category: RECONSTRUCTION
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 1243159
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 59298 / Symmetry type: POINT
Atomic model buildingRef protocol: OTHER / Ref space: REAL
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00719476
ELECTRON MICROSCOPYf_angle_d1.18426432
ELECTRON MICROSCOPYf_dihedral_angle_d12.18511680
ELECTRON MICROSCOPYf_chiral_restr0.0593012
ELECTRON MICROSCOPYf_plane_restr0.0083336

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more