+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8962 | |||||||||
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Title | Cryo-EM structure of rat TRPV6 in complex with Calmodulin | |||||||||
Map data | primary map | |||||||||
Sample |
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Keywords | TRPV6 / TRP channels / Calcium channels / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information parathyroid hormone secretion / TRP channels / calcium-activated cation channel activity / calcium ion import / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor ...parathyroid hormone secretion / TRP channels / calcium-activated cation channel activity / calcium ion import / 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 / PKA activation / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / autophagosome membrane docking / positive regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / regulation of cell communication by electrical coupling involved in cardiac conduction / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Phase 0 - rapid depolarisation / protein phosphatase activator activity / RHO GTPases activate PAKs / calcium ion import across plasma membrane / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / Long-term potentiation / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / DARPP-32 events / detection of calcium ion / Smooth Muscle Contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / RHO GTPases activate IQGAPs / cellular response to interferon-beta / regulation of cardiac muscle contraction / calcium channel inhibitor activity / calcium ion homeostasis / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / voltage-gated potassium channel complex / Activation of AMPK downstream of NMDARs / eNOS activation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Ion homeostasis / positive regulation of protein autophosphorylation / sperm midpiece / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / protein serine/threonine kinase activator activity / sarcomere / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / regulation of cytokinesis / 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 / calcium channel activity / Transcriptional activation of mitochondrial biogenesis / positive regulation of protein serine/threonine kinase activity / Stimuli-sensing channels / spindle pole / cellular response to type II interferon / response to calcium ion / RAS processing / calcium-dependent protein binding / Inactivation, recovery and regulation of the phototransduction cascade / 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 / G2/M transition of mitotic cell cycle Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Rattus norvegicus (Norway rat) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Singh AK / McGoldrick LL | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Sci Adv / Year: 2018 Title: Mechanism of calmodulin inactivation of the calcium-selective TRP channel TRPV6. Authors: Appu K Singh / Luke L McGoldrick / Edward C Twomey / Alexander I Sobolevsky / Abstract: Calcium (Ca) plays a major role in numerous physiological processes. Ca homeostasis is tightly controlled by ion channels, the aberrant regulation of which results in various diseases including ...Calcium (Ca) plays a major role in numerous physiological processes. Ca homeostasis is tightly controlled by ion channels, the aberrant regulation of which results in various diseases including cancers. Calmodulin (CaM)-mediated Ca-induced inactivation is an ion channel regulatory mechanism that protects cells against the toxic effects of Ca overload. We used cryo-electron microscopy to capture the epithelial calcium channel TRPV6 (transient receptor potential vanilloid subfamily member 6) inactivated by CaM. The TRPV6-CaM complex exhibits 1:1 stoichiometry; one TRPV6 tetramer binds both CaM lobes, which adopt a distinct head-to-tail arrangement. The CaM carboxyl-terminal lobe plugs the channel through a unique cation-π interaction by inserting the side chain of lysine K115 into a tetra-tryptophan cage at the pore's intracellular entrance. We propose a mechanism of CaM-mediated Ca-induced inactivation that can be explored for therapeutic design. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8962.map.gz | 49.7 MB | EMDB map data format | |
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Header (meta data) | emd-8962-v30.xml emd-8962.xml | 12.6 KB 12.6 KB | Display Display | EMDB header |
Images | emd_8962.png | 107.7 KB | ||
Filedesc metadata | emd-8962.cif.gz | 5.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8962 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8962 | HTTPS FTP |
-Related structure data
Related structure data | 6e2gMC 8961C 6e2fC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8962.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | primary map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : TRPV6-Calmodulin
Entire | Name: TRPV6-Calmodulin |
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Components |
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-Supramolecule #1: TRPV6-Calmodulin
Supramolecule | Name: TRPV6-Calmodulin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Transient receptor potential cation channel subfamily V member 6
Macromolecule | Name: Transient receptor potential cation channel subfamily V member 6 type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 83.324484 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGWSLPKEKG LILCLWNKFC RWFHRRESWA QSRDEQNLLQ QKRIWESPLL LAAKENNVQA LIKLLKFEGC EVHQKGAMGE TALHIAALY DNLEAAMVLM EAAPELVFEP MTSELYEGQT ALHIAVINQN VNLVRALLAR GASVSARATG SVFHYRPHNL I YYGEHPLS ...String: MGWSLPKEKG LILCLWNKFC RWFHRRESWA QSRDEQNLLQ QKRIWESPLL LAAKENNVQA LIKLLKFEGC EVHQKGAMGE TALHIAALY DNLEAAMVLM EAAPELVFEP MTSELYEGQT ALHIAVINQN VNLVRALLAR GASVSARATG SVFHYRPHNL I YYGEHPLS FAACVGSEEI VRLLIEHGAD IRAQDSLGNT VLHILILQPN KTFACQMYNL LLSYDGGDHL KSLELVPNNQ GL TPFKLAG VEGNIVMFQH LMQKRKHIQW TYGPLTSTLY DLTEIDSSGD DQSLLELIVT TKKREARQIL DQTPVKELVS LKW KRYGRP YFCVLGAIYV LYIICFTMCC VYRPLKPRIT NRTNPRDNTL LQQKLLQEAY VTPKDDLRLV GELVSIVGAV IILL VEIPD IFRLGVTRFF GQTILGGPFH VIIVTYAFMV LVTMVMRLTN SDGEVVPMSF ALVLGWCNVM YFARGFQMLG PFTIM IQKM IFGDLMRFCW LMAVVILGFA SAFYIIFQTE DPDELGHFYD YPMALFSTFE LFLTIIDGPA NYDVDLPFMY SITYAA FAI IATLLMLNLL IAMMGDTHWR VAHERDELWR AQVVATTVML ERKLPRCLWP RSGICGREYG LGDRWFLRVE DRQDLNR QR IRRYAQAFQQ QDDLYSEDLE KDSGEKLEMA RPFGAYLSFP TPSVSRSTSR SSTNWDRLRQ GALRKDLQGI INRGLEDG E GWEYQI UniProtKB: Transient receptor potential cation channel subfamily V member 6 |
-Macromolecule #2: Calmodulin-1
Macromolecule | Name: Calmodulin-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 16.852545 KDa |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
Sequence | String: MADQLTEEQI AEFKEAFSLF DKDGDGTITT KELGTVMRSL GQNPTEAELQ DMINEVDADG NGTIDFPEFL TMMARKMKDT DSEEEIREA FRVFDKDGNG YISAAELRHV MTNLGEKLTD EEVDEMIREA DIDGDGQVNY EEFVQMMTAK UniProtKB: Calmodulin-1 |
-Macromolecule #3: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 6 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.6 mg/mL | |||||||||
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Buffer | pH: 8 Component:
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Grid | Support film - Material: CARBON / Support film - topology: HOLEY / Details: unidentified | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 47.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 507249 |
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Startup model | Type of model: EMDB MAP EMDB ID: |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 111593 |
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | PDB-6e2g: |