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- PDB-6dmu: PI(4,5)P2 bound full-length rbTRPV5 -

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Basic information

Entry
Database: PDB / ID: 6dmu
TitlePI(4,5)P2 bound full-length rbTRPV5
ComponentsTransient receptor potential cation channel subfamily V member 5
KeywordsTRANSPORT PROTEIN / PI(4 / 5)P2 / TRPV5 / full-length / ion channel
Function / homologyAnkyrin repeat / Transient receptor potential cation channel subfamily V member 5/6 / 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 cation channel subfamily V member 5 ...Ankyrin repeat / Transient receptor potential cation channel subfamily V member 5/6 / 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 cation channel subfamily V member 5 / in:ipr004729: / Ion transport domain / calcium ion import across plasma membrane / calcium ion homeostasis / regulation of urine volume / calcium channel activity / calcium ion transmembrane transport / calcium ion transport / protein tetramerization / protein homotetramerization / apical plasma membrane / calmodulin binding / integral component of plasma membrane / metal ion binding / Transient receptor potential cation channel subfamily V member 5
Function and homology information
Specimen sourceOryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4 Å resolution
AuthorsHughes, T.E.T. / Pumroy, R.A. / Moiseenkova-Bell, V.Y.
CitationJournal: Nat Commun / Year: 2018
Title: Structural insights on TRPV5 gating by endogenous modulators.
Authors: Taylor E T Hughes / Ruth A Pumroy / Aysenur Torun Yazici / Marina A Kasimova / Edwin C Fluck / Kevin W Huynh / Amrita Samanta / Sudheer K Molugu / Z Hong Zhou / Vincenzo Carnevale / Tibor Rohacs / Vera Y Moiseenkova-Bell
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 5, 2018 / Release: Oct 24, 2018

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Structure visualization

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Assembly

Deposited unit
A: Transient receptor potential cation channel subfamily V member 5
B: Transient receptor potential cation channel subfamily V member 5
C: Transient receptor potential cation channel subfamily V member 5
D: Transient receptor potential cation channel subfamily V member 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)334,5858
Polyers331,5994
Non-polymers2,9864
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide
Transient receptor potential cation channel subfamily V member 5 / TrpV5 / Epithelial calcium channel 1 / ECaC1 / Osm-9-like TRP channel 3 / OTRPC3


Mass: 82899.656 Da / Num. of mol.: 4 / Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: Trpv5, Ecac1 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q9XSM3
#2: Chemical
ChemComp-PIO / [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate / dioctanoyl l-alpha-phosphatidyl-d-myo-inositol 4,5-diphosphate


Mass: 746.566 Da / Num. of mol.: 4 / Formula: C25H49O19P3

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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

Component
IDNameTypeEntity IDParent IDSource
1PI(4,5)P2-bound rbTRPV5COMPLEX10RECOMBINANT
2rbTRPV5COMPLEX11RECOMBINANT
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1.6 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDVersionCategory
4GctfCTF correction
7Cootmodel fitting
9relioninitial Euler assignment
10relionfinal Euler assignment
11relionclassification
12relion3D reconstruction
13Phenixmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C4
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 25538 / Symmetry type: POINT

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