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- PDB-6dmw: Calmodulin-bound full-length rbTRPV5 -

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Basic information

Entry
Database: PDB / ID: 6dmw
TitleCalmodulin-bound full-length rbTRPV5
Components
  • Calmodulin-1
  • Transient receptor potential cation channel subfamily V member 5
KeywordsTRANSPORT PROTEIN / calmodulin / TRPV5 / full-length / calcium channel
Function / homologyReduction of cytosolic Ca++ levels / Ankyrin repeat-containing domain superfamily / CaMK IV-mediated phosphorylation of CREB / Ankyrin repeat region circular profile. / EF-hand calcium-binding domain profile. / EF-hand calcium-binding domain. / EF-hand domain pair / Ankyrin repeats (3 copies) / Ion transport protein / rt:r-rno-442982: ...Reduction of cytosolic Ca++ levels / Ankyrin repeat-containing domain superfamily / CaMK IV-mediated phosphorylation of CREB / Ankyrin repeat region circular profile. / EF-hand calcium-binding domain profile. / EF-hand calcium-binding domain. / EF-hand domain pair / Ankyrin repeats (3 copies) / Ion transport protein / rt:r-rno-442982: / rt:r-rno-442745: / Calmodulin / Transient receptor potential cation channel subfamily V / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Ankyrin repeat-containing domain / EF-Hand 1, calcium-binding site / EF-hand domain pair / Transient receptor potential cation channel subfamily V member 5 / Transient receptor potential cation channel subfamily V member 5/6 / Sodium/Calcium exchangers / Ion transport domain / Ankyrin repeat / EF-hand domain / Smooth Muscle Contraction / Ankyrin repeat profile. / Calmodulin induced events / eNOS activation / Ca2+ pathway / FCERI mediated Ca+2 mobilization / Stimuli-sensing channels / Ion transport by P-type ATPases / Inactivation, recovery and regulation of the phototransduction cascade / Protein methylation / Glycogen breakdown (glycogenolysis) / RAF/MAP kinase cascade / Cam-PDE 1 activation / RHO GTPases activate IQGAPs / CLEC7A (Dectin-1) induces NFAT activation / Ion homeostasis / RHO GTPases activate PAKs / Phase 0 - rapid depolarisation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / VEGFR2 mediated vascular permeability / Calcineurin activates NFAT / Platelet degranulation / Synthesis of IP3 and IP4 in the cytosol / PKA activation / regulation of store-operated calcium channel activity / calcium ion import across plasma membrane / type 3 metabotropic glutamate receptor binding / establishment of protein localization to mitochondrial membrane / spindle pole body organization / calcium channel regulator activity / calcium ion homeostasis / regulation of high voltage-gated calcium channel activity / regulation of urine volume / regulation of synaptic vesicle endocytosis / establishment of protein localization to membrane / activation of adenylate cyclase activity / N-terminal myristoylation domain binding / positive regulation by host of symbiont cAMP-mediated signal transduction / adenylate cyclase activator activity / positive regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / catalytic complex / nitric-oxide synthase binding / adenylate cyclase binding / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle contraction / regulation of ryanodine-sensitive calcium-release channel activity / calcium channel inhibitor activity / enzyme regulator activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / response to amphetamine / positive regulation of phosphoprotein phosphatase activity / calcium channel complex / calcium channel activity / phosphatidylinositol 3-kinase binding / voltage-gated potassium channel complex / calcium ion transmembrane transport / titin binding / calcium ion transport / regulation of heart rate / sarcomere / calcium-mediated signaling / nitric-oxide synthase regulator activity / regulation of synaptic vesicle exocytosis / calcium-dependent protein binding / regulation of cytokinesis / positive regulation of DNA binding / spindle microtubule / spindle pole / positive regulation of nitric-oxide synthase activity / protein tetramerization / growth cone / protein homotetramerization / disordered domain specific binding
Function and homology information
Specimen sourceOryctolagus cuniculus (rabbit)
Rattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.4 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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Assembly

Deposited unit
A: Transient receptor potential cation channel subfamily V member 5
E: Calmodulin-1
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)348,5718
Polyers348,4515
Non-polymers1203
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: Protein/peptide Calmodulin-1 /


Mass: 16852.545 Da / Num. of mol.: 1 / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Calm1, Calm, Cam, Cam1, CaMI / Production host: Escherichia coli (E. coli) / References: UniProt: P0DP29
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Formula: Ca / Calcium

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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
1Calmodulin-bound rbTRPV5 tetramerCOMPLEX1, 20MULTIPLE SOURCES
2rbTRPV5 tetramerCOMPLEX11RECOMBINANT
3rat CalmodulinCOMPLEX21RECOMBINANT
Molecular weight
IDEntity assembly IDExperimental value
11NO
21NO
31NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
129986Oryctolagus cuniculus (rabbit)
2310116Rattus norvegicus (Norway rat)
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
124932Saccharomyces cerevisiae (baker's yeast)
23562Escherichia coli (E. coli)
Buffer solutionpH: 8.8
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 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 47484 / Symmetry type: POINT

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