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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 transport / water channel activity / : / 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 transport / water channel activity / : / 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 / Calmodulin induced events / regulation of synaptic vesicle endocytosis / 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 / regulation of synaptic vesicle exocytosis / 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 / response to corticosterone / positive regulation of DNA binding / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / 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 / 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 / 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 / adenylate cyclase binding / catalytic complex / positive regulation of cell adhesion / 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 / phosphatidylinositol 3-kinase binding / eNOS activation / enzyme regulator activity / activation of adenylate cyclase activity / 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 / response to amphetamine / substantia nigra development / visual perception / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / nitric-oxide synthase regulator activity / 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 / positive regulation of nitric-oxide synthase activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / spindle microtubule / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT 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
Summary document | 3j41_validation.pdf.gz | 774.3 KB | Display | wwPDB validaton report |
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Full document | 3j41_full_validation.pdf.gz | 817.9 KB | Display | |
Data in XML | 3j41_validation.xml.gz | 38.9 KB | Display | |
Data in CIF | 3j41_validation.cif.gz | 57 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/3j41 ftp://data.pdbj.org/pub/pdb/validation_reports/j4/3j41 | HTTPS FTP |
-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 lens / 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 FIELD / 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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