[English] 日本語
Yorodumi
- PDB-5oeo: Solution structure of the complex of TRPV5(655-725) with a Calmod... -

+
Open data


ID or keywords:

Loading...

-
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 / TRP channels / Calmodulin induced events / Reduction of cytosolic Ca++ levels / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 ...regulation of urine volume / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / TRP channels / Calmodulin induced events / Reduction of cytosolic Ca++ levels / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of cardiac muscle cell action potential / Activation of RAC1 downstream of NMDARs / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of peptidyl-threonine phosphorylation / calcium ion import across plasma membrane / Synthesis of IP3 and IP4 in the cytosol / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / plasma membrane => GO:0005886 / RHO GTPases activate PAKs / : / Ion transport by P-type ATPases / Long-term potentiation / Uptake and function of anthrax toxins / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / catalytic complex / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / cellular response to interferon-beta / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / Protein methylation / eNOS activation / calcium ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Activation of AMPK downstream of NMDARs / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / : / Ion homeostasis / titin binding / regulation of calcium-mediated signaling / positive regulation of protein autophosphorylation / voltage-gated potassium channel complex / sperm midpiece / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / sarcomere / FCERI mediated Ca+2 mobilization / protein serine/threonine kinase activator activity / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / regulation of cytokinesis / positive regulation of peptidyl-threonine phosphorylation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / spindle microtubule / calcium ion transmembrane transport / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT / Transcriptional activation of mitochondrial biogenesis / positive regulation of protein serine/threonine kinase activity / calcium channel activity / Stimuli-sensing channels / cellular response to type II interferon / spindle pole / response to calcium ion / RAS processing / 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-dependent protein binding / G2/M transition of mitotic cell cycle / calcium ion transport / Inactivation, recovery and regulation of the phototransduction cascade / Signaling by BRAF and RAF1 fusions
Similarity search - Function
Transient receptor potential cation channel subfamily V member 5 / Domain of unknown function DUF3447 / Transient receptor potential cation channel subfamily V member 5/6 / Ankyrin repeat / Transient receptor potential cation channel subfamily V / : / EF-hand domain pair / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. ...Transient receptor potential cation channel subfamily V member 5 / Domain of unknown function DUF3447 / Transient receptor potential cation channel subfamily V member 5/6 / Ankyrin repeat / Transient receptor potential cation channel subfamily V / : / EF-hand domain pair / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / EF-hand, calcium binding motif / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
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

-
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

-
NMR measurement

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlc1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more