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- PDB-6bob: Cryo-EM structure of rat TRPV6* in nanodiscs -

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Basic information

Entry
Database: PDB / ID: 6bob
TitleCryo-EM structure of rat TRPV6* in nanodiscs
ComponentsTransient receptor potential cation channel subfamily V member 6
KeywordsTRANSPORT PROTEIN / Ion channel / Membrane protein
Function / homologyAnkyrin repeats (many copies) / in:ipr004729: / Ankyrin repeat region circular profile. / Ankyrin repeat profile. / Ankyrin repeats (3 copies) / Ion transport protein / Ankyrin repeat-containing domain superfamily / Transient receptor potential cation channel subfamily V / Ankyrin repeat-containing domain / Transient receptor potential channel, vanilloid 6 ...Ankyrin repeats (many copies) / in:ipr004729: / Ankyrin repeat region circular profile. / Ankyrin repeat profile. / Ankyrin repeats (3 copies) / Ion transport protein / Ankyrin repeat-containing domain superfamily / Transient receptor potential cation channel subfamily V / Ankyrin repeat-containing domain / Transient receptor potential channel, vanilloid 6 / Transient receptor potential cation channel subfamily V member 5/6 / Ion transport domain / Ankyrin repeat / calcium activated cation channel activity / calcium ion import across plasma membrane / calcium ion import / calcium ion homeostasis / calcium channel activity / calcium ion transmembrane transport / response to calcium ion / protein homotetramerization / apical plasma membrane / calmodulin binding / integral component of plasma membrane / identical protein binding / plasma membrane / metal ion binding / Transient receptor potential cation channel subfamily V member 6
Function and homology information
Specimen sourceRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.9 Å resolution
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
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

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Structure visualization

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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)308,5344
Polyers308,5344
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 77133.492 Da / Num. of mol.: 4 / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Trpv6 / Production host: Homo sapiens (human) / References: UniProt: Q9R186

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: TRPV6* ion channel in closed states / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: HEK-293 cells
Buffer solutionDetails: TRIS, NaCl, / pH: 8
Buffer component
IDConc.FormulaBuffer ID
150 TRIS1
2150 NaCl1
SpecimenConc.: 0.5 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

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 67 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 40

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM softwareName: RELION / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 248836
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 20808 / Symmetry type: POINT
Atomic model buildingRef protocol: OTHER / Ref space: REAL
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00719788
ELECTRON MICROSCOPYf_angle_d1.14026868
ELECTRON MICROSCOPYf_dihedral_angle_d10.59711780
ELECTRON MICROSCOPYf_chiral_restr0.0603056
ELECTRON MICROSCOPYf_plane_restr0.0073396

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