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Yorodumi- PDB-3j41: Pseudo-atomic model of the Aquaporin-0/Calmodulin complex derived... -
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-Basic information
Entry | Database: PDB / ID: 3j41 | ||||||
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Title | Pseudo-atomic model of the Aquaporin-0/Calmodulin complex derived from electron microscopy | ||||||
Components |
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Keywords | TRANSPORT PROTEIN/CALCIUM BINDING / calcium regulation / water channel / membrane protein complex / TRANSPORT PROTEIN-CALCIUM BINDING complex | ||||||
Function / homology | Function and homology information gap junction-mediated intercellular transport / water channel activity / water transport / : / structural constituent of eye lens / gap junction / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / response to stimulus / CaM pathway ...gap junction-mediated intercellular transport / water channel activity / water transport / : / structural constituent of eye lens / gap junction / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / response to stimulus / CaM pathway / response to corticosterone / Cam-PDE 1 activation / Sodium/Calcium exchangers / lens development in camera-type eye / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / regulation of synaptic vesicle endocytosis / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / PKA activation / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / regulation of synaptic vesicle exocytosis / 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 / Negative regulation of NMDA receptor-mediated neuronal transmission / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / Unblocking of NMDA receptors, glutamate binding and activation / regulation of cell communication by electrical coupling involved in cardiac conduction / 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 / Long-term potentiation / positive regulation of phosphoprotein phosphatase activity / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / adenylate cyclase binding / catalytic complex / detection of calcium ion / DARPP-32 events / positive regulation of cell adhesion / 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 / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / positive regulation of DNA binding / Protein methylation / enzyme regulator activity / voltage-gated potassium channel complex / Activation of AMPK downstream of NMDARs / phosphatidylinositol 3-kinase binding / eNOS activation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / response to amphetamine / 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 / activation of adenylate cyclase activity / substantia nigra development / visual perception / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / protein serine/threonine kinase activator activity / regulation of heart rate / nitric-oxide synthase regulator 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 / regulation of cytokinesis / VEGFR2 mediated cell proliferation / positive regulation of nitric-oxide synthase activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / spindle microtubule / mitochondrial membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Ovis aries (sheep) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / negative staining / Resolution: 25 Å | ||||||
Authors | Reichow, S.L. / Clemens, D.M. / Freites, J.A. / Nemeth-Cahalan, K.L. / Heyden, M. / Tobias, D.J. / Hall, J.E. / 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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3j41.cif.gz | 231.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3j41.ent.gz | 182.8 KB | Display | PDB format |
PDBx/mmJSON format | 3j41.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/3j41 ftp://data.pdbj.org/pub/pdb/validation_reports/j4/3j41 | HTTPS FTP |
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-Related structure data
Related structure data | 5679MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 28244.865 Da / Num. of mol.: 4 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Tissue: eye lensLens (anatomy) / References: UniProt: Q6J8I9*PLUS #2: Protein | Mass: 16852.545 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P62158, UniProt: P0DP23*PLUS #3: Chemical | ChemComp-CA / Sequence details | CHAINS A, B, C, AND D (AQUAPORIN) ARE FROM OVIS ARIES, BUT THE MODELED SEQUENCE IS FROM BOS TAURUS ...CHAINS A, B, C, AND D (AQUAPORIN) ARE FROM OVIS ARIES, BUT THE MODELED SEQUENCE IS FROM BOS TAURUS (UNP P06624). | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight | Value: 0.13 MDa / Experimental value: YES | ||||||||||||||||||||
Buffer solution | Name: 25mM HEPES, pH 7.4, 5mM CaCl2, 0.3% decylmaltoside / pH: 7.4 / Details: 25mM HEPES, pH 7.4, 5mM CaCl2, 0.3% decylmaltoside | ||||||||||||||||||||
Specimen | Conc.: 0.02 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO Details: 25mM HEPES, 5mM CaCl2, 0.3% decylmaltoside (Stain Details 0.75% Uranyl Formate) | ||||||||||||||||||||
EM staining | Type: NEGATIVE / Material: Uranyl Formate | ||||||||||||||||||||
Specimen support | Details: 400 mesh carbon coated grid (Ted Pella) |
-Electron microscopy imaging
Microscopy | Model: FEI TECNAI 12 / Date: Feb 25, 2010 |
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Electron gun | Electron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM / Electron beam tilt params: 0 |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 52000 X / Calibrated magnification: 52000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2 mm Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification Camera length: 0 mm |
Specimen holder | Specimen holder model: OTHER / Specimen holder type: FEI Single-Tilt / Tilt angle max: 50 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Image scans | Num. digital images: 200 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: CTF-TILT, each micrograph | |||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | |||||||||||||||
3D reconstruction | Method: Random Conical Tilt / Resolution: 25 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 11720 / Nominal pixel size: 3.98 Å / Actual pixel size: 3.98 Å / Magnification calibration: AQP0 cyrstal Details: Final Map with C2 Symmetry and Filtered to 25 Angstrom (Single particle details: Particles were selected from a tilted pair dataset at 0 and 50 degree tilt using SPIDER. An initial ...Details: Final Map with C2 Symmetry and Filtered to 25 Angstrom (Single particle 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.) (Single particle--Applied symmetry: C2) Symmetry type: POINT | |||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: cross-correlation Details: REFINEMENT PROTOCOL--rigid body DETAILS--A complete model of AQP0-CaM was built by fitting 2B6P and 1NWD into the EM map in Chimera. Loops connecting the two structures were built using COOT ...Details: REFINEMENT PROTOCOL--rigid body DETAILS--A complete model of AQP0-CaM was built by fitting 2B6P and 1NWD into the EM map in Chimera. Loops connecting the two structures were built using COOT and the final model was energy minimized to remove steric clashes. The geometries of the modeled loops (AQP0 residues 222-227) were not refined due to lack of resolution in the experimental map. | |||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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Refinement step | Cycle: LAST
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