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Yorodumi- PDB-3jav: Structure of full-length IP3R1 channel in the apo-state determine... -
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-Basic information
Entry | Database: PDB / ID: 3jav | ||||||
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Title | Structure of full-length IP3R1 channel in the apo-state determined by single particle cryo-EM | ||||||
Components | Inositol 1,4,5-trisphosphate receptor type 1 | ||||||
Keywords | TRANSPORT PROTEIN / inositol 1 / 4 / 5-trisphosphate receptor / calcium release channel / calcium signaling | ||||||
Function / homology | Function and homology information Effects of PIP2 hydrolysis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / inositol 1,4,5-trisphosphate receptor activity involved in regulation of postsynaptic cytosolic calcium levels / release of sequestered calcium ion into cytosol by endoplasmic reticulum / Elevation of cytosolic Ca2+ levels / cGMP effects / smooth endoplasmic reticulum membrane / platelet dense tubular network / calcineurin complex / platelet dense granule membrane ...Effects of PIP2 hydrolysis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / inositol 1,4,5-trisphosphate receptor activity involved in regulation of postsynaptic cytosolic calcium levels / release of sequestered calcium ion into cytosol by endoplasmic reticulum / Elevation of cytosolic Ca2+ levels / cGMP effects / smooth endoplasmic reticulum membrane / platelet dense tubular network / calcineurin complex / platelet dense granule membrane / epithelial fluid transport / ion channel modulating, G protein-coupled receptor signaling pathway / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / inositol 1,4,5-trisphosphate-gated calcium channel activity / calcium import into the mitochondrion / regulation of postsynaptic cytosolic calcium ion concentration / voluntary musculoskeletal movement / inositol 1,4,5 trisphosphate binding / positive regulation of calcium ion transport / negative regulation of calcium-mediated signaling / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / endoplasmic reticulum calcium ion homeostasis / positive regulation of hepatocyte proliferation / nuclear inner membrane / transport vesicle membrane / Ion homeostasis / dendrite development / intracellularly gated calcium channel activity / ligand-gated ion channel signaling pathway / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / single fertilization / GABA-ergic synapse / calcium channel inhibitor activity / cellular response to cAMP / release of sequestered calcium ion into cytosol / regulation of cytosolic calcium ion concentration / liver regeneration / phosphatidylinositol binding / secretory granule membrane / post-embryonic development / sarcoplasmic reticulum / synaptic membrane / calcium ion transmembrane transport / calcium-mediated signaling / cell morphogenesis / positive regulation of insulin secretion / Schaffer collateral - CA1 synapse / positive regulation of neuron projection development / nuclear envelope / calcium ion transport / presynapse / cellular response to hypoxia / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / protein phosphatase binding / protein homotetramerization / transmembrane transporter binding / postsynapse / postsynaptic density / response to hypoxia / protein domain specific binding / positive regulation of apoptotic process / neuronal cell body / synapse / dendrite / calcium ion binding / endoplasmic reticulum membrane / negative regulation of apoptotic process / protein-containing complex binding / nucleolus / perinuclear region of cytoplasm / endoplasmic reticulum / protein-containing complex / ATP binding / identical protein binding / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 Å | ||||||
Authors | Fan, G. / Baker, M.L. / Wang, Z. / Baker, M.R. / Sinyagovskiy, P.A. / Chiu, W. / Ludtke, S.J. / Serysheva, I.I. | ||||||
Citation | Journal: Nature / Year: 2015 Title: Gating machinery of InsP3R channels revealed by electron cryomicroscopy. Authors: Guizhen Fan / Matthew L Baker / Zhao Wang / Mariah R Baker / Pavel A Sinyagovskiy / Wah Chiu / Steven J Ludtke / Irina I Serysheva / Abstract: Inositol-1,4,5-trisphosphate receptors (InsP3Rs) are ubiquitous ion channels responsible for cytosolic Ca(2+) signalling and essential for a broad array of cellular processes ranging from contraction ...Inositol-1,4,5-trisphosphate receptors (InsP3Rs) are ubiquitous ion channels responsible for cytosolic Ca(2+) signalling and essential for a broad array of cellular processes ranging from contraction to secretion, and from proliferation to cell death. Despite decades of research on InsP3Rs, a mechanistic understanding of their structure-function relationship is lacking. Here we present the first, to our knowledge, near-atomic (4.7 Å) resolution electron cryomicroscopy structure of the tetrameric mammalian type 1 InsP3R channel in its apo-state. At this resolution, we are able to trace unambiguously ∼85% of the protein backbone, allowing us to identify the structural elements involved in gating and modulation of this 1.3-megadalton channel. Although the central Ca(2+)-conduction pathway is similar to other ion channels, including the closely related ryanodine receptor, the cytosolic carboxy termini are uniquely arranged in a left-handed α-helical bundle, directly interacting with the amino-terminal domains of adjacent subunits. This configuration suggests a molecular mechanism for allosteric regulation of channel gating by intracellular signals. | ||||||
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 | 3jav.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3jav.ent.gz | 580 KB | Display | PDB format |
PDBx/mmJSON format | 3jav.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jav_validation.pdf.gz | 800.5 KB | Display | wwPDB validaton report |
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Full document | 3jav_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3jav_validation.xml.gz | 205.9 KB | Display | |
Data in CIF | 3jav_validation.cif.gz | 296.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/3jav ftp://data.pdbj.org/pub/pdb/validation_reports/ja/3jav | HTTPS FTP |
-Related structure data
Related structure data | 6369MC 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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1 |
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-Components
#1: Protein | Mass: 313657.406 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P29994 |
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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 | Name: Inositol 1,4,5-trisphosphate receptor, type 1 / Type: COMPLEX / Details: homotetramer |
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Molecular weight | Value: 1.3 MDa / Experimental value: NO |
Buffer solution | Name: 50 mM Tris-HCl, 0.4% CHAPS, 150 mM NaCl, 1 mM DTT, 1 mM EGTA, 1 mM EDTA pH: 7.4 Details: 50 mM Tris-HCl, 0.4% CHAPS, 150 mM NaCl, 1 mM DTT, 1 mM EGTA, 1 mM EDTA |
Specimen | Conc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: 400 mesh copper grids with thin carbon support |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temp: 120 K / Humidity: 100 % Details: Blot once for 3 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV). Method: blot once for 3 seconds |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 / Date: Jan 1, 2014 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 23000 X / Calibrated magnification: 30886 X / Nominal defocus max: 3500 nm / Nominal defocus min: 600 nm / Cs: 2 mm Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification. |
Specimen holder | Specimen holder model: GATAN LIQUID NITROGEN / Temperature: 100 K / Temperature (max): 102 K / Temperature (min): 95 K |
Image recording | Electron dose: 22 e/Å2 / Film or detector model: GATAN K2 (4k x 4k) |
EM imaging optics | Energyfilter name: FEI |
Image scans | Num. digital images: 4160 |
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: CTFFIND3 | ||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||
3D reconstruction | Method: K-means clustering / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 96106 / Nominal pixel size: 1.62 Å / Actual pixel size: 1.62 Å / Details: Applied symmetry: C4 / Symmetry type: POINT | ||||||||||||
Refinement step | Cycle: LAST
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