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- PDB-5oeo: Solution structure of the complex of TRPV5(655-725) with a Calmod... -

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Basic information

Entry
Database: PDB / ID: 5oeo
TitleSolution structure of the complex of TRPV5(655-725) with a Calmodulin E32Q/E68Q double mutant
Components
  • Calmodulin-1
  • Transient receptor potential cation channel subfamily V member 5
KeywordsMEMBRANE PROTEIN / TRPV5 / calcium channel / dynamics / calmodulin / regulation
Function / homology
Function and homology information


regulation of urine volume / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase ...regulation of urine volume / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / TRP channels / PKA activation / CaMK IV-mediated phosphorylation of CREB / negative regulation of high voltage-gated calcium channel activity / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / presynaptic endocytosis / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of ryanodine-sensitive calcium-release channel activity / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / calcineurin-mediated signaling / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / calcium ion import across plasma membrane / Long-term potentiation / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / protein phosphatase activator activity / regulation of ryanodine-sensitive calcium-release channel activity / DARPP-32 events / Smooth Muscle Contraction / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / presynaptic cytosol / calcium channel inhibitor activity / cellular response to interferon-beta / Protein methylation / calcium ion homeostasis / Activation of AMPK downstream of NMDARs / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / eNOS activation / regulation of calcium-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / titin binding / voltage-gated potassium channel complex / sperm midpiece / substantia nigra development / calcium channel complex / calyx of Held / FCERI mediated Ca+2 mobilization / Ras activation upon Ca2+ influx through NMDA receptor / FCGR3A-mediated IL10 synthesis / adenylate cyclase activator activity / regulation of heart rate / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / protein serine/threonine kinase activator activity / VEGFR2 mediated cell proliferation / sarcomere / regulation of cytokinesis / VEGFR2 mediated vascular permeability / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / spindle microtubule / RAF activation / Transcriptional activation of mitochondrial biogenesis / calcium ion transmembrane transport / calcium channel activity / Stimuli-sensing channels / cellular response to type II interferon / long-term synaptic potentiation / response to calcium ion / RAS processing / spindle pole / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / calcium ion transport / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / Signaling by BRAF and RAF1 fusions / Inactivation, recovery and regulation of the phototransduction cascade / Platelet degranulation / myelin sheath / Ca2+ pathway
Similarity search - Function
Transient receptor potential cation channel subfamily V member 5 / Transient receptor potential cation channel subfamily V member 5/6 / Transient receptor potential cation channel subfamily V / EF-hand / : / Recoverin; domain 1 / Ankyrin repeat / EF-hand domain pair / Ankyrin repeats (3 copies) / Ankyrin repeat profile. ...Transient receptor potential cation channel subfamily V member 5 / Transient receptor potential cation channel subfamily V member 5/6 / Transient receptor potential cation channel subfamily V / EF-hand / : / Recoverin; domain 1 / Ankyrin repeat / EF-hand domain pair / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / EF-hand, calcium binding motif / Ankyrin repeat-containing domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calmodulin-1 / Transient receptor potential cation channel subfamily V member 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing / molecular dynamics
AuthorsVuister, G.W. / Bokhovchuk, F.M. / Bate, N. / Kovalevskaya, N. / Goult, B.T. / Spronk, C.A.E.M.
Funding support United Kingdom, Netherlands, 5items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J007897/1 United Kingdom
Medical Research Council (United Kingdom)MR/L000555/1 United Kingdom
Medical Research Council (United Kingdom)MR/P00038X/1 United Kingdom
NWO700.55.443 Netherlands
NWO700.57.101 Netherlands
CitationJournal: Biochemistry / Year: 2018
Title: The Structural Basis of Calcium-Dependent Inactivation of the Transient Receptor Potential Vanilloid 5 Channel.
Authors: Bokhovchuk, F.M. / Bate, N. / Kovalevskaya, N.V. / Goult, B.T. / Spronk, C.A.E.M. / Vuister, G.W.
History
DepositionJul 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calmodulin-1
C: Transient receptor potential cation channel subfamily V member 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7404
Polymers24,6602
Non-polymers802
Water00
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, isothermal titration calorimetry, NMR
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1680 Å2
ΔGint-29 kcal/mol
Surface area17450 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 120structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein Calmodulin-1


Mass: 16937.652 Da / Num. of mol.: 1 / Mutation: E32Q, E68Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0DP23
#2: Protein Transient receptor potential cation channel subfamily V member 5 / TrpV5 / Calcium transport protein 2 / CaT2 / Epithelial calcium channel 1 / ECaC1 / Osm-9-like TRP ...TrpV5 / Calcium transport protein 2 / CaT2 / Epithelial calcium channel 1 / ECaC1 / Osm-9-like TRP channel 3 / OTRPC3


Mass: 7722.194 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRPV5, ECAC1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9NQA5
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic33D 1H-15N NOESY
121isotropic33D 1H-13C NOESY aliphatic
131isotropic33D 1H-13C NOESY aromatic
142isotropic33D 1H-13C NOESY aliphatic

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1220 uM 13C/15N Calmodulin, 220 uM hTRPV5(655-725), 95% H2O/5% D2O1:1 13C15N-CaM12 : hTRPV5655-725Sample 195% H2O/5% D2O
solution2380 uM [U-99% 15N] Calmodulin, 380 uM [U-99% 13C; U-99% 15N] hTRPV5(655-725), 95% H2O/5% D2O1:1 15N-CaM12 : 13C15N-hTRPV5655-725Sample 295% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
220 uMCalmodulin13C/15N1
220 uMhTRPV5(655-725)1
380 uMCalmodulin[U-99% 15N]2
380 uMhTRPV5(655-725)[U-99% 13C; U-99% 15N]2
Sample conditionsIonic strength: 84 mM / Ionic strength err: 0.01 / Label: NMR Buffer / pH: 7.4 / PH err: 0.1 / Pressure: 1 atm / Pressure err: 0.1 / Temperature: 308 K / Temperature err: 0.1

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVIBrukerAVI5001
Bruker AVIIIBrukerAVIII6002
Bruker AVIIBrukerAVII8003

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.4CCPNchemical shift assignment
AnalysisAssign3CCPNchemical shift assignment
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
CcpNmr Analysis2.4CCPNpeak picking
YASARA15.6Yasara Biosciences; Krieger et al.refinement
NMRPipe7.9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipe7.9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Refinement
MethodSoftware ordinalDetails
simulated annealing2
molecular dynamics6Refinement using log-normal potentials as described by Bordeaux et al, 2011
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 120 / Conformers submitted total number: 20

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