+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5679 | |||||||||
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Title | Electron Microscopy of the Aquaporin-0/Calmodulin Complex | |||||||||
Map data | 3D Reconstruction of the Aquaporin-0/Calmodulin Complex | |||||||||
Sample |
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Keywords | aquaporin / calmodulin / calcium regulation / water channel / membrane protein complex / electron microscopy | |||||||||
Function / homology | Function and homology information gap junction-mediated intercellular transport / water channel activity / water transport / : / structural constituent of eye lens / establishment of protein localization to mitochondrial membrane / gap junction / type 3 metabotropic glutamate receptor binding / CaM pathway / Cam-PDE 1 activation ...gap junction-mediated intercellular transport / water channel activity / water transport / : / structural constituent of eye lens / establishment of protein localization to mitochondrial membrane / gap junction / type 3 metabotropic glutamate receptor binding / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / lens development in camera-type eye / response to stimulus / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / regulation of synaptic vesicle endocytosis / 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 / regulation of synaptic vesicle exocytosis / 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 / response to corticosterone / positive regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / nitric-oxide synthase binding / 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 / 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 / adenylate cyclase binding / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / DARPP-32 events / detection of calcium ion / positive regulation of cell adhesion / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / positive regulation of DNA binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / enzyme regulator activity / voltage-gated potassium channel complex / phosphatidylinositol 3-kinase binding / 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 / response to amphetamine / calcium channel complex / activation of adenylate cyclase activity / substantia nigra development / adenylate cyclase activator activity / visual perception / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / nitric-oxide synthase regulator activity / 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 / positive regulation of nitric-oxide synthase activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / spindle microtubule / mitochondrial membrane Similarity search - Function | |||||||||
Biological species | Ovis aries (sheep) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 25.0 Å | |||||||||
Authors | Reichow SL / Clemens DM / Freites JA / Nemeth-Cahalan KL / Heyden M / Tobias DJ / Hall JE / Gonen T | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2013 Title: Allosteric mechanism of water-channel gating by Ca2+-calmodulin. Authors: Steve L Reichow / Daniel M Clemens / J Alfredo Freites / Karin L Németh-Cahalan / Matthias Heyden / Douglas J Tobias / James E Hall / Tamir Gonen / Abstract: Calmodulin (CaM) is a universal regulatory protein that communicates the presence of calcium to its molecular targets and correspondingly modulates their function. This key signaling protein is ...Calmodulin (CaM) is a universal regulatory protein that communicates the presence of calcium to its molecular targets and correspondingly modulates their function. This key signaling protein is important for controlling the activity of hundreds of membrane channels and transporters. However, understanding of the structural mechanisms driving CaM regulation of full-length membrane proteins has remained elusive. In this study, we determined the pseudoatomic structure of full-length mammalian aquaporin-0 (AQP0, Bos taurus) in complex with CaM, using EM to elucidate how this signaling protein modulates water-channel function. Molecular dynamics and functional mutation studies reveal how CaM binding inhibits AQP0 water permeability by allosterically closing the cytoplasmic gate of AQP0. Our mechanistic model provides new insight, only possible in the context of the fully assembled channel, into how CaM regulates multimeric channels by facilitating cooperativity between adjacent subunits. | |||||||||
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_5679.map.gz | 458.7 KB | EMDB map data format | |
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Header (meta data) | emd-5679-v30.xml emd-5679.xml | 13.2 KB 13.2 KB | Display Display | EMDB header |
Images | emd_5679.tif | 287.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5679 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5679 | HTTPS FTP |
-Related structure data
Related structure data | 3j41MC 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_5679.map.gz / Format: CCP4 / Size: 1.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 3D Reconstruction of the Aquaporin-0/Calmodulin Complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.98 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 : Aquaporin-0 bound to Calmodulin
Entire | Name: Aquaporin-0 bound to Calmodulin |
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Components |
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-Supramolecule #1000: Aquaporin-0 bound to Calmodulin
Supramolecule | Name: Aquaporin-0 bound to Calmodulin / type: sample / ID: 1000 Details: Sample was prepared for electron microscopy with negative stain Oligomeric state: One tetramer of Aquaporin-0 bound to 2 molecules of Calmodulin Number unique components: 2 |
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Molecular weight | Experimental: 130 KDa / Theoretical: 130 KDa / Method: Size-exclusion Chromatography and SDS-PAGE |
-Macromolecule #1: Aquaporin-0
Macromolecule | Name: Aquaporin-0 / type: protein_or_peptide / ID: 1 / Name.synonym: AQP0, MIP / Details: Crosslinked to Calmodulin using EDC/NHS / Number of copies: 4 / Oligomeric state: tetramer / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Ovis aries (sheep) / synonym: Sheep / Tissue: eye lens / Cell: fiber cell / Location in cell: plasma membrane |
Molecular weight | Experimental: 25 KDa / Theoretical: 25 KDa |
Sequence | UniProtKB: Pas12 / InterPro: Major intrinsic protein |
-Macromolecule #2: Calmodulin
Macromolecule | Name: Calmodulin / type: protein_or_peptide / ID: 2 / Name.synonym: CaM / Details: Calmodulin crosslinked to Aquaporin-0 / Number of copies: 2 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Location in cell: cytoplasmic |
Molecular weight | Experimental: 17 KDa / Theoretical: 17 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: BL21 / Recombinant plasmid: pET |
Sequence | UniProtKB: Calmodulin-3 |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.02 mg/mL |
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Buffer | pH: 7.4 / Details: 25mM HEPES, 5mM CaCl2, 0.3% decylmaltoside |
Staining | Type: NEGATIVE / Details: 0.75% uranyl formate |
Grid | Details: 400 mesh carbon coated grid (Ted Pella) |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI 12 |
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Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Calibrated magnification: 52000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 52000 |
Sample stage | Specimen holder model: OTHER / Tilt angle max: 50 |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification Legacy - Electron beam tilt params: 0 |
Date | Feb 25, 2010 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 200 / Average electron dose: 15 e/Å2 / Bits/pixel: 16 |
Tilt angle min | 0 |
-Image processing
CTF correction | Details: CTF-TILT, each micrograph |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER, FREALIGN Details: Final Map with C2 Symmetry and Filtered to 25 Angstrom Number images used: 11720 |
Details | Particles were selected from a tilted pair dataset at 0 and 50 degree tilt using SPIDER. An initial reconstruction was generated using random conical tilt methods in SPIDER and refined in FREALIGN |