+Open data
-Basic information
Entry | Database: PDB / ID: 6mu2 | |||||||||||||||||||||
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Title | Structure of full-length IP3R1 channel in the Apo-state | |||||||||||||||||||||
Components | Inositol 1,4,5-trisphosphate receptor type 1 | |||||||||||||||||||||
Keywords | MEMBRANE PROTEIN / inositol 1 / 4 / 5-trisphosphate receptor / calcium release channel / neuronal type 1 | |||||||||||||||||||||
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: 3.9 Å | |||||||||||||||||||||
Authors | Serysheva, I.I. / Fan, G. / Baker, M.R. / Wang, Z. / Seryshev, A. / Ludtke, S.J. / Baker, M.L. | |||||||||||||||||||||
Funding support | United States, 6items
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Citation | Journal: Cell Res / Year: 2018 Title: Cryo-EM reveals ligand induced allostery underlying InsPR channel gating. Authors: Guizhen Fan / Mariah R Baker / Zhao Wang / Alexander B Seryshev / Steven J Ludtke / Matthew L Baker / Irina I Serysheva / Abstract: Inositol-1,4,5-trisphosphate receptors (InsPRs) are cation channels that mobilize Ca from intracellular stores in response to a wide range of cellular stimuli. The paradigm of InsPR activation is the ...Inositol-1,4,5-trisphosphate receptors (InsPRs) are cation channels that mobilize Ca from intracellular stores in response to a wide range of cellular stimuli. The paradigm of InsPR activation is the coupled interplay between binding of InsP and Ca that switches the ion conduction pathway between closed and open states to enable the passage of Ca through the channel. However, the molecular mechanism of how the receptor senses and decodes ligand-binding signals into gating motion remains unknown. Here, we present the electron cryo-microscopy structure of InsPR1 from rat cerebellum determined to 4.1 Å resolution in the presence of activating concentrations of Ca and adenophostin A (AdA), a structural mimetic of InsP and the most potent known agonist of the channel. Comparison with the 3.9 Å-resolution structure of InsPR1 in the Apo-state, also reported herein, reveals the binding arrangement of AdA in the tetrameric channel assembly and striking ligand-induced conformational rearrangements within cytoplasmic domains coupled to the dilation of a hydrophobic constriction at the gate. Together, our results provide critical insights into the mechanistic principles by which ligand-binding allosterically gates InsPR channel. | |||||||||||||||||||||
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 | 6mu2.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6mu2.ent.gz | 990.3 KB | Display | PDB format |
PDBx/mmJSON format | 6mu2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6mu2_validation.pdf.gz | 909.3 KB | Display | wwPDB validaton report |
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Full document | 6mu2_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6mu2_validation.xml.gz | 254.4 KB | Display | |
Data in CIF | 6mu2_validation.cif.gz | 379.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mu/6mu2 ftp://data.pdbj.org/pub/pdb/validation_reports/mu/6mu2 | HTTPS FTP |
-Related structure data
Related structure data | 9244MC 9243C 9245C 9246C 9247C 9248C 6mu1C 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) / Organ: Brain / Tissue: cerebellum / 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: COMPLEX / Details: tetrameric assembly / Entity ID: all / Source: NATURAL |
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Molecular weight | Value: 1.3 MDa / Experimental value: NO |
Source (natural) | Organism: Rattus norvegicus (Norway rat) / Cellular location: membrane / Organ: Brain / Organelle: endoplasmic reticulum / Tissue: Cerebellum |
Buffer solution | pH: 7.4 Details: 50 mM Tris-HCl buffer (pH 7.4), 150 mM NaCl, 1 mM DTT, 0.4% CHAPS, 2 mM EGTA, 1 mM EDTA, protease inhibitors |
Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Monodisperse sample |
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F30 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Specimen holder | Cryogen: NITROGEN Specimen holder model: GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER Temperature (max): 93 K / Temperature (min): 93 K |
Image recording | Average exposure time: 0.2 sec. / Electron dose: 1.3 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 9823 |
Image scans | Movie frames/image: 30 / Used frames/image: 2-17 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 207914 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 65438 Details: Image processing was performed independently using RELION and EMAN2 to near-atomic resolution in large regions of the structure. Local resolution assessment performed independently for each ...Details: Image processing was performed independently using RELION and EMAN2 to near-atomic resolution in large regions of the structure. Local resolution assessment performed independently for each map revealed different domains were better resolved by each software package. To avoid human bias and extract the most information from each reconstruction the final map was a locally filtered average of the EMAN2 and RELION map. To combine the two maps, a local resolution filter, based on a windowed FSC local resolution assessment, was performed independently on the two maps. The two locally filtered maps were then averaged together. The local filtration determines the contribution of each map at each resolution in each region of the final composite map, permitting each map to dominate in regions where better self-consistency was obtained during refinement. Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL |