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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 / homologyEF-hand calcium-binding domain. / Transient receptor potential cation channel subfamily V / Ankyrin repeat profile. / EF-hand domain / Ankyrin repeat / Ion transport domain / Transient receptor potential cation channel subfamily V member 5/6 / Transient receptor potential cation channel subfamily V member 5 / EF-hand domain pair / EF-Hand 1, calcium-binding site ...EF-hand calcium-binding domain. / Transient receptor potential cation channel subfamily V / Ankyrin repeat profile. / EF-hand domain / Ankyrin repeat / Ion transport domain / Transient receptor potential cation channel subfamily V member 5/6 / Transient receptor potential cation channel subfamily V member 5 / EF-hand domain pair / EF-Hand 1, calcium-binding site / Ankyrin repeat-containing domain / EF-hand calcium-binding domain profile. / in:ipr004729: / Ankyrin repeat-containing domain superfamily / EF-hand domain pair / Calmodulin / Ion transport protein / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / regulation of store-operated calcium channel activity / calcium ion import across plasma membrane / calcium ion homeostasis / calcium channel regulator activity / regulation of urine volume / establishment of protein localization to membrane / type 3 metabotropic glutamate receptor binding / establishment of protein localization to mitochondrial membrane / positive regulation by host of symbiont cAMP-mediated signal transduction / N-terminal myristoylation domain binding / regulation of synaptic vesicle endocytosis / regulation of high voltage-gated calcium channel activity / protein phosphatase activator activity / adenylate cyclase activator activity / positive regulation of ryanodine-sensitive calcium-release channel activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / catalytic complex / activation of adenylate cyclase activity / adenylate cyclase binding / enzyme regulator activity / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle contraction / voltage-gated potassium channel complex / calcium channel activity / calcium channel inhibitor activity / nitric-oxide synthase binding / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / positive regulation of phosphoprotein phosphatase activity / calcium channel complex / calcium ion transmembrane transport / sarcomere / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / calcium ion transport / response to amphetamine / regulation of heart rate / phosphatidylinositol 3-kinase binding / calcium-mediated signaling / positive regulation of DNA binding / spindle microtubule / regulation of cytokinesis / regulation of synaptic vesicle exocytosis / nitric-oxide synthase regulator activity / calcium-dependent protein binding / spindle pole / protein tetramerization / positive regulation of nitric-oxide synthase activity / growth cone / protein homotetramerization / disordered domain specific binding / G2/M transition of mitotic cell cycle / apical plasma membrane / protein N-terminus binding / ion channel binding / calmodulin binding / neuron projection / centrosome / myelin sheath / protein domain specific binding / protein kinase binding / calcium ion binding / integral component of plasma membrane / mitochondrion / nucleoplasm / plasma membrane / nucleus / metal ion binding / cytosol / cytoplasm / Calmodulin-1 / Transient receptor potential cation channel subfamily V member 5
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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