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- PDB-6bo9: Cryo-EM structure of human TRPV6 in amphipols -

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Database: PDB / ID: 6bo9
TitleCryo-EM structure of human TRPV6 in amphipols
ComponentsTransient receptor potential cation channel subfamily V member 6
KeywordsTRANSPORT PROTEIN / Ion channel / Membrane protein
Specimen sourceHomo sapiens / human /
MethodElectron microscopy (4 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.
CitationNature, 2018, 553, 233-237

Nature, 2018, 553, 233-237 Yorodumi Papers
Opening of the human epithelial calcium channel TRPV6.
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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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)340,6764

TypeNameSymmetry operationNumber
identity operation1_5551


#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: 85168.953 Da / Num. of mol.: 4 / Source: (gene. exp.) Homo sapiens / human / / Gene: TRPV6, ECAC2 / Production host: Homo sapiens / References: UniProt: Q9H1D0

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

Sample preparation

ComponentName: TRPV6 ion channel in open 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
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: 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 FIELD
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


SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM softwareName: RELION / Category: RECONSTRUCTION
Particle selectionNumber of particles selected: 306784
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 65259 / Symmetry type: POINT
Atomic model buildingRef protocol: OTHER / Ref space: REAL
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00719484
ELECTRON MICROSCOPYf_angle_d1.10126440
ELECTRON MICROSCOPYf_dihedral_angle_d12.52811688
ELECTRON MICROSCOPYf_chiral_restr0.0553012
ELECTRON MICROSCOPYf_plane_restr0.0073336

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